Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_143209_700
Start time	2017-01-06 14:32:09
Run time	1 day 23:06:21.958
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF250, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF250/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170106_143209_700/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_143209_700/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_143209_700/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_143209_700/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_143209_700/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_143209_700/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_143209_700/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_143209_700/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_143209_700/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_143209_700/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_143209_700/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_143209_700/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_143209_700/task.graphviz.report.line_97.id_24
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_spp.spp_rep1.line_57.id_10
Name	spp rep1
Thread	thread_Root
PID	24251

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

Start	2017-01-06 14:32:14
End	2017-01-08 13:32:48
Elapsed	1 day 23:00:33
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_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/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
Dependencies

 
# SYS command. line 59

 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 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_1.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
34148 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_1.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_1.nodup.tagAlign.gz 
opened /tmp/24251.1.amd.q/RtmpKRrzwH/SRR1370877_1.nodup.tagAlign86c83c08cc8d
done. read 12425809 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24251.1.amd.q/RtmpKRrzwH/input15MReadsNSCLess1.05.50MSubsample.tagAlign86c8115d6a94
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1488151 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.162713737272067 
Top 3 estimates for fragment length 160 
Window half size 305 
Phantom peak location 55 
Phantom peak Correlation 0.1560563 
Normalized Strand cross-correlation coefficient (NSC) 1.093396 
Relative Strand cross-correlation Coefficient (RSC) 1.919391 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 4.101579  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2438086  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000092 
Detected 402177 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70164	70468	.	0	.	22.5598004088712	-1	4.09436629833613	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70164	70468	.	0	.	22.5598004088712	-1	4.09436629833613	152

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24252

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

Start	2017-01-06 14:32:15
End	2017-01-06 17:49:51
Elapsed	03:17:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/signal/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/signal/macs2/rep1/SRR1370877_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/ZNF250/out/align/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/align/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1 -o "SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/signal/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/align/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1 -o "SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/signal/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_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--------------------
34152 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:32:48: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_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  @ Fri, 06 Jan 2017 14:32:48: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:32:48: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:32:56:  1000000 
INFO  @ Fri, 06 Jan 2017 14:33:02:  2000000 
INFO  @ Fri, 06 Jan 2017 14:33:08:  3000000 
INFO  @ Fri, 06 Jan 2017 14:33:14:  4000000 
INFO  @ Fri, 06 Jan 2017 14:33:20:  5000000 
INFO  @ Fri, 06 Jan 2017 14:33:26:  6000000 
INFO  @ Fri, 06 Jan 2017 14:33:32:  7000000 
INFO  @ Fri, 06 Jan 2017 14:33:38:  8000000 
INFO  @ Fri, 06 Jan 2017 14:33:44:  9000000 
INFO  @ Fri, 06 Jan 2017 14:33:50:  10000000 
INFO  @ Fri, 06 Jan 2017 14:33:56:  11000000 
INFO  @ Fri, 06 Jan 2017 14:34:02:  12000000 
INFO  @ Fri, 06 Jan 2017 14:34:05: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:34:11:  1000000 
INFO  @ Fri, 06 Jan 2017 14:34:17:  2000000 
INFO  @ Fri, 06 Jan 2017 14:34:23:  3000000 
INFO  @ Fri, 06 Jan 2017 14:34:29:  4000000 
INFO  @ Fri, 06 Jan 2017 14:34:35:  5000000 
INFO  @ Fri, 06 Jan 2017 14:34:41:  6000000 
INFO  @ Fri, 06 Jan 2017 14:34:47:  7000000 
INFO  @ Fri, 06 Jan 2017 14:34:53:  8000000 
INFO  @ Fri, 06 Jan 2017 14:34:59:  9000000 
INFO  @ Fri, 06 Jan 2017 14:35:06:  10000000 
INFO  @ Fri, 06 Jan 2017 14:35:12:  11000000 
INFO  @ Fri, 06 Jan 2017 14:35:18:  12000000 
INFO  @ Fri, 06 Jan 2017 14:35:24:  13000000 
INFO  @ Fri, 06 Jan 2017 14:35:30:  14000000 
INFO  @ Fri, 06 Jan 2017 14:35:36:  15000000 
INFO  @ Fri, 06 Jan 2017 14:35:42:  16000000 
INFO  @ Fri, 06 Jan 2017 14:35:48:  17000000 
INFO  @ Fri, 06 Jan 2017 14:35:54:  18000000 
INFO  @ Fri, 06 Jan 2017 14:36:00:  19000000 
INFO  @ Fri, 06 Jan 2017 14:36:06:  20000000 
INFO  @ Fri, 06 Jan 2017 14:36:12:  21000000 
INFO  @ Fri, 06 Jan 2017 14:36:18:  22000000 
INFO  @ Fri, 06 Jan 2017 14:36:24:  23000000 
INFO  @ Fri, 06 Jan 2017 14:36:30:  24000000 
INFO  @ Fri, 06 Jan 2017 14:36:36:  25000000 
INFO  @ Fri, 06 Jan 2017 14:36:42:  26000000 
INFO  @ Fri, 06 Jan 2017 14:36:48:  27000000 
INFO  @ Fri, 06 Jan 2017 14:36:54:  28000000 
INFO  @ Fri, 06 Jan 2017 14:37:00:  29000000 
INFO  @ Fri, 06 Jan 2017 14:37:06:  30000000 
INFO  @ Fri, 06 Jan 2017 14:37:12:  31000000 
INFO  @ Fri, 06 Jan 2017 14:37:18:  32000000 
INFO  @ Fri, 06 Jan 2017 14:37:24:  33000000 
INFO  @ Fri, 06 Jan 2017 14:37:30:  34000000 
INFO  @ Fri, 06 Jan 2017 14:37:36:  35000000 
INFO  @ Fri, 06 Jan 2017 14:37:42:  36000000 
INFO  @ Fri, 06 Jan 2017 14:37:48:  37000000 
INFO  @ Fri, 06 Jan 2017 14:37:54:  38000000 
INFO  @ Fri, 06 Jan 2017 14:38:01:  39000000 
INFO  @ Fri, 06 Jan 2017 14:38:07:  40000000 
INFO  @ Fri, 06 Jan 2017 14:38:14:  41000000 
INFO  @ Fri, 06 Jan 2017 14:38:20:  42000000 
INFO  @ Fri, 06 Jan 2017 14:38:26:  43000000 
INFO  @ Fri, 06 Jan 2017 14:38:33:  44000000 
INFO  @ Fri, 06 Jan 2017 14:38:40:  45000000 
INFO  @ Fri, 06 Jan 2017 14:38:46:  46000000 
INFO  @ Fri, 06 Jan 2017 14:38:53:  47000000 
INFO  @ Fri, 06 Jan 2017 14:38:59:  48000000 
INFO  @ Fri, 06 Jan 2017 14:39:06:  49000000 
INFO  @ Fri, 06 Jan 2017 14:39:12:  50000000 
INFO  @ Fri, 06 Jan 2017 14:39:16: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 14:39:16: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 14:39:16: #1  total tags in treatment: 12425809 
INFO  @ Fri, 06 Jan 2017 14:39:16: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:39:16: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:39:16: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:39:16: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:39:16: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:39:16: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:39:16: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:39:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:48:17: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:48:17: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:48:17: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:48:17: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:48:17: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:09:35: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:09:40: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:09:44: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:09:46: Done! 
INFO  @ Fri, 06 Jan 2017 15:09:56: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_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/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_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  @ Fri, 06 Jan 2017 15:09:56: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:09:56: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:10:04:  1000000 
INFO  @ Fri, 06 Jan 2017 15:10:13:  2000000 
INFO  @ Fri, 06 Jan 2017 15:10:22:  3000000 
INFO  @ Fri, 06 Jan 2017 15:10:30:  4000000 
INFO  @ Fri, 06 Jan 2017 15:10:38:  5000000 
INFO  @ Fri, 06 Jan 2017 15:10:46:  6000000 
INFO  @ Fri, 06 Jan 2017 15:10:54:  7000000 
INFO  @ Fri, 06 Jan 2017 15:11:02:  8000000 
INFO  @ Fri, 06 Jan 2017 15:11:10:  9000000 
INFO  @ Fri, 06 Jan 2017 15:11:18:  10000000 
INFO  @ Fri, 06 Jan 2017 15:11:27:  11000000 
INFO  @ Fri, 06 Jan 2017 15:11:35:  12000000 
INFO  @ Fri, 06 Jan 2017 15:11:39: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:11:48:  1000000 
INFO  @ Fri, 06 Jan 2017 15:11:57:  2000000 
INFO  @ Fri, 06 Jan 2017 15:12:06:  3000000 
INFO  @ Fri, 06 Jan 2017 15:12:14:  4000000 
INFO  @ Fri, 06 Jan 2017 15:12:22:  5000000 
INFO  @ Fri, 06 Jan 2017 15:12:31:  6000000 
INFO  @ Fri, 06 Jan 2017 15:12:38:  7000000 
INFO  @ Fri, 06 Jan 2017 15:12:47:  8000000 
INFO  @ Fri, 06 Jan 2017 15:12:55:  9000000 
INFO  @ Fri, 06 Jan 2017 15:13:03:  10000000 
INFO  @ Fri, 06 Jan 2017 15:13:11:  11000000 
INFO  @ Fri, 06 Jan 2017 15:13:19:  12000000 
INFO  @ Fri, 06 Jan 2017 15:13:27:  13000000 
INFO  @ Fri, 06 Jan 2017 15:13:35:  14000000 
INFO  @ Fri, 06 Jan 2017 15:13:43:  15000000 
INFO  @ Fri, 06 Jan 2017 15:13:51:  16000000 
INFO  @ Fri, 06 Jan 2017 15:14:00:  17000000 
INFO  @ Fri, 06 Jan 2017 15:14:08:  18000000 
INFO  @ Fri, 06 Jan 2017 15:14:16:  19000000 
INFO  @ Fri, 06 Jan 2017 15:14:24:  20000000 
INFO  @ Fri, 06 Jan 2017 15:14:32:  21000000 
INFO  @ Fri, 06 Jan 2017 15:14:40:  22000000 
INFO  @ Fri, 06 Jan 2017 15:14:47:  23000000 
INFO  @ Fri, 06 Jan 2017 15:14:56:  24000000 
INFO  @ Fri, 06 Jan 2017 15:15:03:  25000000 
INFO  @ Fri, 06 Jan 2017 15:15:12:  26000000 
INFO  @ Fri, 06 Jan 2017 15:15:20:  27000000 
INFO  @ Fri, 06 Jan 2017 15:15:28:  28000000 
INFO  @ Fri, 06 Jan 2017 15:15:35:  29000000 
INFO  @ Fri, 06 Jan 2017 15:15:44:  30000000 
INFO  @ Fri, 06 Jan 2017 15:15:52:  31000000 
INFO  @ Fri, 06 Jan 2017 15:16:00:  32000000 
INFO  @ Fri, 06 Jan 2017 15:16:09:  33000000 
INFO  @ Fri, 06 Jan 2017 15:16:16:  34000000 
INFO  @ Fri, 06 Jan 2017 15:16:24:  35000000 
INFO  @ Fri, 06 Jan 2017 15:16:32:  36000000 
INFO  @ Fri, 06 Jan 2017 15:16:40:  37000000 
INFO  @ Fri, 06 Jan 2017 15:16:48:  38000000 
INFO  @ Fri, 06 Jan 2017 15:16:56:  39000000 
INFO  @ Fri, 06 Jan 2017 15:17:03:  40000000 
INFO  @ Fri, 06 Jan 2017 15:17:11:  41000000 
INFO  @ Fri, 06 Jan 2017 15:17:19:  42000000 
INFO  @ Fri, 06 Jan 2017 15:17:27:  43000000 
INFO  @ Fri, 06 Jan 2017 15:17:35:  44000000 
INFO  @ Fri, 06 Jan 2017 15:17:43:  45000000 
INFO  @ Fri, 06 Jan 2017 15:17:51:  46000000 
INFO  @ Fri, 06 Jan 2017 15:17:59:  47000000 
INFO  @ Fri, 06 Jan 2017 15:18:07:  48000000 
INFO  @ Fri, 06 Jan 2017 15:18:15:  49000000 
INFO  @ Fri, 06 Jan 2017 15:18:22:  50000000 
INFO  @ Fri, 06 Jan 2017 15:18:26: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:18:26: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:18:26: #1  total tags in treatment: 12425809 
INFO  @ Fri, 06 Jan 2017 15:18:26: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:18:26: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:18:26: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:18:26: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:18:26: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:18:26: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:18:26: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:18:26: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:27:49: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:36:43: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:37:03: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:37:17: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:37:31: Done! 
INFO  @ Fri, 06 Jan 2017 15:38:09: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:40:02: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:48:38: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:51:13: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:14:35: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:22:42: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:37:09: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:39:09: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:47:16: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:49:49: Values in your input bedGraph files will be multiplied by 12.425809 ... 
INFO  @ Fri, 06 Jan 2017 17:12:03: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:14:12: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:28:08: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'!

Num	3
ID	task.callpeak_spp.spp_rep1_pr1.line_57.id_12
Name	spp rep1-pr1
Thread	thread_Root
PID	24253

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

Start	2017-01-06 14:32:16
End	2017-01-08 06:49:01
Elapsed	1 day 16:16:44
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
Dependencies

 
# SYS command. line 59

 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 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
34151 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz 
opened /tmp/24253.1.amd.q/Rtmp2OQ9v3/SRR1370877_1.nodup.pr1.tagAlign86d94f55b0cf
done. read 6212905 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24253.1.amd.q/Rtmp2OQ9v3/input15MReadsNSCLess1.05.50MSubsample.tagAlign86d9222f317b
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.0812323 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.0888881130571986 
Top 3 estimates for fragment length 160 
Window half size 300 
Phantom peak location 50 
Phantom peak Correlation 0.08522151 
Normalized Strand cross-correlation coefficient (NSC) 1.094246 
Relative Strand cross-correlation Coefficient (RSC) 1.91913 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 8.148369  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.122724  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000143 
Detected 162271 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70185	70485	.	0	.	13.2592687456243	-1	3.89437145385624	150

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70185	70485	.	0	.	13.2592687456243	-1	3.89437145385624	150

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24254

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

Start	2017-01-06 14:32:18
End	2017-01-08 09:19:20
Elapsed	1 day 18:47:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
Dependencies

 
# SYS command. line 59

 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 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
34149 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz 
opened /tmp/24254.1.amd.q/Rtmp1fjywH/SRR1370877_1.nodup.pr2.tagAlign86c79044dec
done. read 6212904 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24254.1.amd.q/Rtmp1fjywH/input15MReadsNSCLess1.05.50MSubsample.tagAlign86c75bdc76d
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.08103037 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.0886373878715395 
Top 3 estimates for fragment length 160 
Window half size 310 
Phantom peak location 55 
Phantom peak Correlation 0.08498357 
Normalized Strand cross-correlation coefficient (NSC) 1.093879 
Relative Strand cross-correlation Coefficient (RSC) 1.924269 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 8.14639  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1227538  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000031 
Detected 165537 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70127	70437	.	0	.	8.57576777910169	-1	4.05304000864275	155

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70127	70437	.	0	.	8.57576777910169	-1	4.05304000864275	155

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24255

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

Start	2017-01-06 14:32:18
End	2017-01-06 15:30:53
Elapsed	00:58:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
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/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370877_1.nodup.pr1.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.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--------------------
34150 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:32:48: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 14:32:48: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:32:48: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:32:56:  1000000 
INFO  @ Fri, 06 Jan 2017 14:33:02:  2000000 
INFO  @ Fri, 06 Jan 2017 14:33:08:  3000000 
INFO  @ Fri, 06 Jan 2017 14:33:14:  4000000 
INFO  @ Fri, 06 Jan 2017 14:33:20:  5000000 
INFO  @ Fri, 06 Jan 2017 14:33:27:  6000000 
INFO  @ Fri, 06 Jan 2017 14:33:28: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:33:34:  1000000 
INFO  @ Fri, 06 Jan 2017 14:33:40:  2000000 
INFO  @ Fri, 06 Jan 2017 14:33:46:  3000000 
INFO  @ Fri, 06 Jan 2017 14:33:53:  4000000 
INFO  @ Fri, 06 Jan 2017 14:33:59:  5000000 
INFO  @ Fri, 06 Jan 2017 14:34:05:  6000000 
INFO  @ Fri, 06 Jan 2017 14:34:11:  7000000 
INFO  @ Fri, 06 Jan 2017 14:34:17:  8000000 
INFO  @ Fri, 06 Jan 2017 14:34:23:  9000000 
INFO  @ Fri, 06 Jan 2017 14:34:29:  10000000 
INFO  @ Fri, 06 Jan 2017 14:34:35:  11000000 
INFO  @ Fri, 06 Jan 2017 14:34:41:  12000000 
INFO  @ Fri, 06 Jan 2017 14:34:47:  13000000 
INFO  @ Fri, 06 Jan 2017 14:34:53:  14000000 
INFO  @ Fri, 06 Jan 2017 14:34:59:  15000000 
INFO  @ Fri, 06 Jan 2017 14:35:05:  16000000 
INFO  @ Fri, 06 Jan 2017 14:35:11:  17000000 
INFO  @ Fri, 06 Jan 2017 14:35:17:  18000000 
INFO  @ Fri, 06 Jan 2017 14:35:23:  19000000 
INFO  @ Fri, 06 Jan 2017 14:35:29:  20000000 
INFO  @ Fri, 06 Jan 2017 14:35:35:  21000000 
INFO  @ Fri, 06 Jan 2017 14:35:41:  22000000 
INFO  @ Fri, 06 Jan 2017 14:35:47:  23000000 
INFO  @ Fri, 06 Jan 2017 14:35:53:  24000000 
INFO  @ Fri, 06 Jan 2017 14:35:59:  25000000 
INFO  @ Fri, 06 Jan 2017 14:36:05:  26000000 
INFO  @ Fri, 06 Jan 2017 14:36:11:  27000000 
INFO  @ Fri, 06 Jan 2017 14:36:17:  28000000 
INFO  @ Fri, 06 Jan 2017 14:36:23:  29000000 
INFO  @ Fri, 06 Jan 2017 14:36:29:  30000000 
INFO  @ Fri, 06 Jan 2017 14:36:35:  31000000 
INFO  @ Fri, 06 Jan 2017 14:36:41:  32000000 
INFO  @ Fri, 06 Jan 2017 14:36:47:  33000000 
INFO  @ Fri, 06 Jan 2017 14:36:53:  34000000 
INFO  @ Fri, 06 Jan 2017 14:36:58:  35000000 
INFO  @ Fri, 06 Jan 2017 14:37:04:  36000000 
INFO  @ Fri, 06 Jan 2017 14:37:10:  37000000 
INFO  @ Fri, 06 Jan 2017 14:37:16:  38000000 
INFO  @ Fri, 06 Jan 2017 14:37:22:  39000000 
INFO  @ Fri, 06 Jan 2017 14:37:28:  40000000 
INFO  @ Fri, 06 Jan 2017 14:37:35:  41000000 
INFO  @ Fri, 06 Jan 2017 14:37:41:  42000000 
INFO  @ Fri, 06 Jan 2017 14:37:47:  43000000 
INFO  @ Fri, 06 Jan 2017 14:37:53:  44000000 
INFO  @ Fri, 06 Jan 2017 14:37:59:  45000000 
INFO  @ Fri, 06 Jan 2017 14:38:05:  46000000 
INFO  @ Fri, 06 Jan 2017 14:38:11:  47000000 
INFO  @ Fri, 06 Jan 2017 14:38:17:  48000000 
INFO  @ Fri, 06 Jan 2017 14:38:24:  49000000 
INFO  @ Fri, 06 Jan 2017 14:38:30:  50000000 
INFO  @ Fri, 06 Jan 2017 14:38:33: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 14:38:33: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 14:38:33: #1  total tags in treatment: 6212905 
INFO  @ Fri, 06 Jan 2017 14:38:33: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:38:33: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:38:33: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:38:33: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:38:33: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:38:33: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:38:33: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:38:33: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:46:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:46:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:46:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:46:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:46:24: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:03:19: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:03:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:03:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:03:31: Done! 
INFO  @ Fri, 06 Jan 2017 15:03:42: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 15:03:42: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:03:42: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:03:52:  1000000 
INFO  @ Fri, 06 Jan 2017 15:04:00:  2000000 
INFO  @ Fri, 06 Jan 2017 15:04:08:  3000000 
INFO  @ Fri, 06 Jan 2017 15:04:16:  4000000 
INFO  @ Fri, 06 Jan 2017 15:04:25:  5000000 
INFO  @ Fri, 06 Jan 2017 15:04:33:  6000000 
INFO  @ Fri, 06 Jan 2017 15:04:35: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:04:43:  1000000 
INFO  @ Fri, 06 Jan 2017 15:04:51:  2000000 
INFO  @ Fri, 06 Jan 2017 15:04:58:  3000000 
INFO  @ Fri, 06 Jan 2017 15:05:06:  4000000 
INFO  @ Fri, 06 Jan 2017 15:05:14:  5000000 
INFO  @ Fri, 06 Jan 2017 15:05:21:  6000000 
INFO  @ Fri, 06 Jan 2017 15:05:29:  7000000 
INFO  @ Fri, 06 Jan 2017 15:05:37:  8000000 
INFO  @ Fri, 06 Jan 2017 15:05:44:  9000000 
INFO  @ Fri, 06 Jan 2017 15:05:52:  10000000 
INFO  @ Fri, 06 Jan 2017 15:06:00:  11000000 
INFO  @ Fri, 06 Jan 2017 15:06:08:  12000000 
INFO  @ Fri, 06 Jan 2017 15:06:15:  13000000 
INFO  @ Fri, 06 Jan 2017 15:06:23:  14000000 
INFO  @ Fri, 06 Jan 2017 15:06:31:  15000000 
INFO  @ Fri, 06 Jan 2017 15:06:38:  16000000 
INFO  @ Fri, 06 Jan 2017 15:06:46:  17000000 
INFO  @ Fri, 06 Jan 2017 15:06:53:  18000000 
INFO  @ Fri, 06 Jan 2017 15:07:03:  19000000 
INFO  @ Fri, 06 Jan 2017 15:07:10:  20000000 
INFO  @ Fri, 06 Jan 2017 15:07:18:  21000000 
INFO  @ Fri, 06 Jan 2017 15:07:25:  22000000 
INFO  @ Fri, 06 Jan 2017 15:07:33:  23000000 
INFO  @ Fri, 06 Jan 2017 15:07:41:  24000000 
INFO  @ Fri, 06 Jan 2017 15:07:48:  25000000 
INFO  @ Fri, 06 Jan 2017 15:07:56:  26000000 
INFO  @ Fri, 06 Jan 2017 15:08:03:  27000000 
INFO  @ Fri, 06 Jan 2017 15:08:12:  28000000 
INFO  @ Fri, 06 Jan 2017 15:08:19:  29000000 
INFO  @ Fri, 06 Jan 2017 15:08:27:  30000000 
INFO  @ Fri, 06 Jan 2017 15:08:35:  31000000 
INFO  @ Fri, 06 Jan 2017 15:08:43:  32000000 
INFO  @ Fri, 06 Jan 2017 15:08:50:  33000000 
INFO  @ Fri, 06 Jan 2017 15:08:58:  34000000 
INFO  @ Fri, 06 Jan 2017 15:09:06:  35000000 
INFO  @ Fri, 06 Jan 2017 15:09:13:  36000000 
INFO  @ Fri, 06 Jan 2017 15:09:21:  37000000 
INFO  @ Fri, 06 Jan 2017 15:09:29:  38000000 
INFO  @ Fri, 06 Jan 2017 15:09:36:  39000000 
INFO  @ Fri, 06 Jan 2017 15:09:44:  40000000 
INFO  @ Fri, 06 Jan 2017 15:09:52:  41000000 
INFO  @ Fri, 06 Jan 2017 15:10:00:  42000000 
INFO  @ Fri, 06 Jan 2017 15:10:08:  43000000 
INFO  @ Fri, 06 Jan 2017 15:10:16:  44000000 
INFO  @ Fri, 06 Jan 2017 15:10:23:  45000000 
INFO  @ Fri, 06 Jan 2017 15:10:31:  46000000 
INFO  @ Fri, 06 Jan 2017 15:10:38:  47000000 
INFO  @ Fri, 06 Jan 2017 15:10:46:  48000000 
INFO  @ Fri, 06 Jan 2017 15:10:54:  49000000 
INFO  @ Fri, 06 Jan 2017 15:11:02:  50000000 
INFO  @ Fri, 06 Jan 2017 15:11:06: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:11:06: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:11:06: #1  total tags in treatment: 6212905 
INFO  @ Fri, 06 Jan 2017 15:11:06: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:11:06: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:11:06: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:11:06: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:11:06: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:11:06: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:11:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:11:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:19:20: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:29:15: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:29:40: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:29:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:30:16: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24327

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

Start	2017-01-06 15:30:55
End	2017-01-06 16:29:51
Elapsed	00:58:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
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/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370877_1.nodup.pr2.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.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/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.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--------------------
41948 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:31:18: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 15:31:18: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:31:18: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:31:25:  1000000 
INFO  @ Fri, 06 Jan 2017 15:31:33:  2000000 
INFO  @ Fri, 06 Jan 2017 15:31:41:  3000000 
INFO  @ Fri, 06 Jan 2017 15:31:49:  4000000 
INFO  @ Fri, 06 Jan 2017 15:31:56:  5000000 
INFO  @ Fri, 06 Jan 2017 15:32:04:  6000000 
INFO  @ Fri, 06 Jan 2017 15:32:06: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:32:14:  1000000 
INFO  @ Fri, 06 Jan 2017 15:32:21:  2000000 
INFO  @ Fri, 06 Jan 2017 15:32:29:  3000000 
INFO  @ Fri, 06 Jan 2017 15:32:37:  4000000 
INFO  @ Fri, 06 Jan 2017 15:32:44:  5000000 
INFO  @ Fri, 06 Jan 2017 15:32:52:  6000000 
INFO  @ Fri, 06 Jan 2017 15:32:59:  7000000 
INFO  @ Fri, 06 Jan 2017 15:33:07:  8000000 
INFO  @ Fri, 06 Jan 2017 15:33:15:  9000000 
INFO  @ Fri, 06 Jan 2017 15:33:22:  10000000 
INFO  @ Fri, 06 Jan 2017 15:33:30:  11000000 
INFO  @ Fri, 06 Jan 2017 15:33:37:  12000000 
INFO  @ Fri, 06 Jan 2017 15:33:44:  13000000 
INFO  @ Fri, 06 Jan 2017 15:33:52:  14000000 
INFO  @ Fri, 06 Jan 2017 15:33:59:  15000000 
INFO  @ Fri, 06 Jan 2017 15:34:07:  16000000 
INFO  @ Fri, 06 Jan 2017 15:34:14:  17000000 
INFO  @ Fri, 06 Jan 2017 15:34:22:  18000000 
INFO  @ Fri, 06 Jan 2017 15:34:29:  19000000 
INFO  @ Fri, 06 Jan 2017 15:34:36:  20000000 
INFO  @ Fri, 06 Jan 2017 15:34:44:  21000000 
INFO  @ Fri, 06 Jan 2017 15:34:51:  22000000 
INFO  @ Fri, 06 Jan 2017 15:34:59:  23000000 
INFO  @ Fri, 06 Jan 2017 15:35:06:  24000000 
INFO  @ Fri, 06 Jan 2017 15:35:14:  25000000 
INFO  @ Fri, 06 Jan 2017 15:35:21:  26000000 
INFO  @ Fri, 06 Jan 2017 15:35:28:  27000000 
INFO  @ Fri, 06 Jan 2017 15:35:36:  28000000 
INFO  @ Fri, 06 Jan 2017 15:35:43:  29000000 
INFO  @ Fri, 06 Jan 2017 15:35:51:  30000000 
INFO  @ Fri, 06 Jan 2017 15:35:58:  31000000 
INFO  @ Fri, 06 Jan 2017 15:36:06:  32000000 
INFO  @ Fri, 06 Jan 2017 15:36:13:  33000000 
INFO  @ Fri, 06 Jan 2017 15:36:20:  34000000 
INFO  @ Fri, 06 Jan 2017 15:36:28:  35000000 
INFO  @ Fri, 06 Jan 2017 15:36:35:  36000000 
INFO  @ Fri, 06 Jan 2017 15:36:43:  37000000 
INFO  @ Fri, 06 Jan 2017 15:36:50:  38000000 
INFO  @ Fri, 06 Jan 2017 15:36:58:  39000000 
INFO  @ Fri, 06 Jan 2017 15:37:05:  40000000 
INFO  @ Fri, 06 Jan 2017 15:37:12:  41000000 
INFO  @ Fri, 06 Jan 2017 15:37:20:  42000000 
INFO  @ Fri, 06 Jan 2017 15:37:27:  43000000 
INFO  @ Fri, 06 Jan 2017 15:37:35:  44000000 
INFO  @ Fri, 06 Jan 2017 15:37:42:  45000000 
INFO  @ Fri, 06 Jan 2017 15:37:50:  46000000 
INFO  @ Fri, 06 Jan 2017 15:37:57:  47000000 
INFO  @ Fri, 06 Jan 2017 15:38:05:  48000000 
INFO  @ Fri, 06 Jan 2017 15:38:12:  49000000 
INFO  @ Fri, 06 Jan 2017 15:38:19:  50000000 
INFO  @ Fri, 06 Jan 2017 15:38:23: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:38:23: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:38:23: #1  total tags in treatment: 6212904 
INFO  @ Fri, 06 Jan 2017 15:38:23: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:38:23: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:38:23: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:38:23: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:38:23: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:38:23: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:38:23: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:38:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:46:53: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:46:53: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:46:53: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:46:53: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:46:53: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:03:17: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:03:21: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 16:03:25: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 16:03:27: Done! 
INFO  @ Fri, 06 Jan 2017 16:03:34: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 16:03:34: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 16:03:34: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 16:03:42:  1000000 
INFO  @ Fri, 06 Jan 2017 16:03:50:  2000000 
INFO  @ Fri, 06 Jan 2017 16:03:58:  3000000 
INFO  @ Fri, 06 Jan 2017 16:04:06:  4000000 
INFO  @ Fri, 06 Jan 2017 16:04:13:  5000000 
INFO  @ Fri, 06 Jan 2017 16:04:21:  6000000 
INFO  @ Fri, 06 Jan 2017 16:04:23: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 16:04:30:  1000000 
INFO  @ Fri, 06 Jan 2017 16:04:37:  2000000 
INFO  @ Fri, 06 Jan 2017 16:04:45:  3000000 
INFO  @ Fri, 06 Jan 2017 16:04:52:  4000000 
INFO  @ Fri, 06 Jan 2017 16:05:00:  5000000 
INFO  @ Fri, 06 Jan 2017 16:05:09:  6000000 
INFO  @ Fri, 06 Jan 2017 16:05:16:  7000000 
INFO  @ Fri, 06 Jan 2017 16:05:23:  8000000 
INFO  @ Fri, 06 Jan 2017 16:05:30:  9000000 
INFO  @ Fri, 06 Jan 2017 16:05:37:  10000000 
INFO  @ Fri, 06 Jan 2017 16:05:45:  11000000 
INFO  @ Fri, 06 Jan 2017 16:05:52:  12000000 
INFO  @ Fri, 06 Jan 2017 16:05:59:  13000000 
INFO  @ Fri, 06 Jan 2017 16:06:06:  14000000 
INFO  @ Fri, 06 Jan 2017 16:06:14:  15000000 
INFO  @ Fri, 06 Jan 2017 16:06:21:  16000000 
INFO  @ Fri, 06 Jan 2017 16:06:28:  17000000 
INFO  @ Fri, 06 Jan 2017 16:06:36:  18000000 
INFO  @ Fri, 06 Jan 2017 16:06:43:  19000000 
INFO  @ Fri, 06 Jan 2017 16:06:50:  20000000 
INFO  @ Fri, 06 Jan 2017 16:06:57:  21000000 
INFO  @ Fri, 06 Jan 2017 16:07:05:  22000000 
INFO  @ Fri, 06 Jan 2017 16:07:12:  23000000 
INFO  @ Fri, 06 Jan 2017 16:07:19:  24000000 
INFO  @ Fri, 06 Jan 2017 16:07:26:  25000000 
INFO  @ Fri, 06 Jan 2017 16:07:33:  26000000 
INFO  @ Fri, 06 Jan 2017 16:07:40:  27000000 
INFO  @ Fri, 06 Jan 2017 16:07:48:  28000000 
INFO  @ Fri, 06 Jan 2017 16:07:55:  29000000 
INFO  @ Fri, 06 Jan 2017 16:08:02:  30000000 
INFO  @ Fri, 06 Jan 2017 16:08:09:  31000000 
INFO  @ Fri, 06 Jan 2017 16:08:17:  32000000 
INFO  @ Fri, 06 Jan 2017 16:08:25:  33000000 
INFO  @ Fri, 06 Jan 2017 16:08:34:  34000000 
INFO  @ Fri, 06 Jan 2017 16:08:41:  35000000 
INFO  @ Fri, 06 Jan 2017 16:08:49:  36000000 
INFO  @ Fri, 06 Jan 2017 16:08:56:  37000000 
INFO  @ Fri, 06 Jan 2017 16:09:03:  38000000 
INFO  @ Fri, 06 Jan 2017 16:09:11:  39000000 
INFO  @ Fri, 06 Jan 2017 16:09:19:  40000000 
INFO  @ Fri, 06 Jan 2017 16:09:26:  41000000 
INFO  @ Fri, 06 Jan 2017 16:09:34:  42000000 
INFO  @ Fri, 06 Jan 2017 16:09:41:  43000000 
INFO  @ Fri, 06 Jan 2017 16:09:49:  44000000 
INFO  @ Fri, 06 Jan 2017 16:09:56:  45000000 
INFO  @ Fri, 06 Jan 2017 16:10:04:  46000000 
INFO  @ Fri, 06 Jan 2017 16:10:11:  47000000 
INFO  @ Fri, 06 Jan 2017 16:10:18:  48000000 
INFO  @ Fri, 06 Jan 2017 16:10:24:  49000000 
INFO  @ Fri, 06 Jan 2017 16:10:32:  50000000 
INFO  @ Fri, 06 Jan 2017 16:10:36: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 16:10:36: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 16:10:36: #1  total tags in treatment: 6212904 
INFO  @ Fri, 06 Jan 2017 16:10:36: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 16:10:36: #1 finished! 
INFO  @ Fri, 06 Jan 2017 16:10:36: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 16:10:36: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 16:10:36: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 16:10:36: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 16:10:36: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 16:10:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:18:46: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:28:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:28:34: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:28:57: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:29:13: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24418

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

Start	2017-01-08 13:32:49
End	2017-01-08 13:34:08
Elapsed	00:01:19
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Dependencies

 
# SYS command. line 61

 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 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8199 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1	70185	70485	.	0	.	13.2592687456243	-1	3.89437145385624	150

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1	70185	70485	.	0	.	13.2592687456243	-1	3.89437145385624	150

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	70127	70437	.	0	.	8.57576777910169	-1	4.05304000864275	155

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000195.1	70127	70437	.	0	.	8.57576777910169	-1	4.05304000864275	155

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70164	70468	.	0	.	22.5598004088712	-1	4.09436629833613	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70164	70468	.	0	.	22.5598004088712	-1	4.09436629833613	152

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24420

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

Start	2017-01-08 13:34:10
End	2017-01-08 13:35:32
Elapsed	00:01:22
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 75

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 77

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370877_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370877_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR

# SYS command. line 81

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 84

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 97

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8317 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.27 1.28 0.82 0.37]
Number of reported peaks - 38060/38060 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 6171/38060 (16.2%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24421

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

Start	2017-01-08 13:35:33
End	2017-01-08 13:36:52
Elapsed	00:01:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/qc/ZNF250_IDR_final.qc
Dependencies

 
# SYS command. line 221

 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 223

 echo -e "Nt\tN1	N2	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/qc/ZNF250_IDR_final.qc

# SYS command. line 224

 echo -e "0\t430	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/qc/ZNF250_IDR_final.qc

# SYS command. line 226

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8468 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	10
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21
Name	blacklist_filter peak 1
Thread	thread_Root
PID	41980

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

Start	2017-01-08 13:36:54
End	2017-01-08 13:38:02
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 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 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
41984 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70164	70468	.	0	.	22.5598004088712	-1	4.09436629833613	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/rep1/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	70164	70468	.	0	.	22.5598004088712	-1	4.09436629833613	152

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	45545

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

Start	2017-01-08 13:38:03
End	2017-01-08 13:38:12
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.hammock.gz
Dependencies

 
# SYS command. line 414

 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 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/spp/overlap/SRR1370877_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
45549 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	46189

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

Start	2017-01-08 13:38:13
End	2017-01-08 13:38:22
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 414

 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 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/peak/idr/pseudo_reps/rep1/ZNF250_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
46193 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	46729

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

Start	2017-01-08 13:38:23
End	2017-01-08 13:38:31
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 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 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/report/ZNF250_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/report/ZNF250_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/report/ZNF250_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
46734 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/ascp/3.5.6:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/homer/default
bool	allowEmpty	false
string[]	args	[-title, ZNF250, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF250/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250/out/align/rep1/SRR1370877_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
string	ASCPKEY	/software/ascp/etc/asperaweb_id_dsa.openssh
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:10.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_veRoBQ
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:ascp/3.5.6:sratoolkit/2.5.2:homer/default
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	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/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/software/sratoolkit/2.5.2/bin/:/software/ascp/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/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:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF250
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/ZNF250
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 43899 22
string	SSH_CONNECTION	171.65.77.8 43899 171.65.76.63 22
string	SSH_TTY	/dev/pts/0
string	STY	39229.ZNF250.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
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	1080
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope