Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_144104_234
Start time	2017-01-06 14:41:04
Run time	1 day 13:51:27.399
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF454, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF454/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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_144104_234/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_144104_234/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_144104_234/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_144104_234/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_144104_234/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_144104_234/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_144104_234/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_144104_234/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_144104_234/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_144104_234/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_144104_234/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_144104_234/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_144104_234/task.graphviz.report.line_97.id_24
thread_41	thread_Root
thread_42	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	24285

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

Start	2017-01-06 14:41:10
End	2017-01-08 04:27:10
Elapsed	1 day 13:45:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_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--------------------
37868 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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 150 
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/ZNF454/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/align/rep1/SRR1370908_1.nodup.tagAlign.gz 
opened /tmp/24285.1.amd.q/RtmpouDFoC/SRR1370908_1.nodup.tagAlign94a3649e9350
done. read 15924789 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24285.1.amd.q/RtmpouDFoC/input15MReadsNSCLess1.05.50MSubsample.tagAlign94a321819498
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1821073 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.189392974712506 
Top 3 estimates for fragment length 150 
Window half size 225 
Phantom peak location 70 
Phantom peak Correlation 0.1858366 
Normalized Strand cross-correlation coefficient (NSC) 1.040007 
Relative Strand cross-correlation Coefficient (RSC) 1.95364 
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= 3.14204  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.3182646  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000012 
Detected 477113 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/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2581	2805	.	0	.	46.5875372222257	-1	3.67860941655892	112

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2581	2805	.	0	.	46.5875372222257	-1	3.67860941655892	112

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24286

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

Start	2017-01-06 14:41:11
End	2017-01-06 18:00:13
Elapsed	03:19:01
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/signal/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/signal/macs2/rep1/SRR1370908_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/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1 -o "SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/signal/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1 -o "SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/signal/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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--------------------
37870 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:41:30: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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 14:41:30: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:41:30: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:41:37:  1000000 
INFO  @ Fri, 06 Jan 2017 14:41:45:  2000000 
INFO  @ Fri, 06 Jan 2017 14:41:52:  3000000 
INFO  @ Fri, 06 Jan 2017 14:41:59:  4000000 
INFO  @ Fri, 06 Jan 2017 14:42:06:  5000000 
INFO  @ Fri, 06 Jan 2017 14:42:13:  6000000 
INFO  @ Fri, 06 Jan 2017 14:42:21:  7000000 
INFO  @ Fri, 06 Jan 2017 14:42:28:  8000000 
INFO  @ Fri, 06 Jan 2017 14:42:35:  9000000 
INFO  @ Fri, 06 Jan 2017 14:42:42:  10000000 
INFO  @ Fri, 06 Jan 2017 14:42:50:  11000000 
INFO  @ Fri, 06 Jan 2017 14:42:57:  12000000 
INFO  @ Fri, 06 Jan 2017 14:43:04:  13000000 
INFO  @ Fri, 06 Jan 2017 14:43:12:  14000000 
INFO  @ Fri, 06 Jan 2017 14:43:20:  15000000 
INFO  @ Fri, 06 Jan 2017 14:43:28: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:43:35:  1000000 
INFO  @ Fri, 06 Jan 2017 14:43:43:  2000000 
INFO  @ Fri, 06 Jan 2017 14:43:51:  3000000 
INFO  @ Fri, 06 Jan 2017 14:43:59:  4000000 
INFO  @ Fri, 06 Jan 2017 14:44:06:  5000000 
INFO  @ Fri, 06 Jan 2017 14:44:14:  6000000 
INFO  @ Fri, 06 Jan 2017 14:44:22:  7000000 
INFO  @ Fri, 06 Jan 2017 14:44:30:  8000000 
INFO  @ Fri, 06 Jan 2017 14:44:37:  9000000 
INFO  @ Fri, 06 Jan 2017 14:44:45:  10000000 
INFO  @ Fri, 06 Jan 2017 14:44:52:  11000000 
INFO  @ Fri, 06 Jan 2017 14:45:00:  12000000 
INFO  @ Fri, 06 Jan 2017 14:45:08:  13000000 
INFO  @ Fri, 06 Jan 2017 14:45:15:  14000000 
INFO  @ Fri, 06 Jan 2017 14:45:23:  15000000 
INFO  @ Fri, 06 Jan 2017 14:45:31:  16000000 
INFO  @ Fri, 06 Jan 2017 14:45:39:  17000000 
INFO  @ Fri, 06 Jan 2017 14:45:47:  18000000 
INFO  @ Fri, 06 Jan 2017 14:45:56:  19000000 
INFO  @ Fri, 06 Jan 2017 14:46:04:  20000000 
INFO  @ Fri, 06 Jan 2017 14:46:12:  21000000 
INFO  @ Fri, 06 Jan 2017 14:46:20:  22000000 
INFO  @ Fri, 06 Jan 2017 14:46:28:  23000000 
INFO  @ Fri, 06 Jan 2017 14:46:36:  24000000 
INFO  @ Fri, 06 Jan 2017 14:46:44:  25000000 
INFO  @ Fri, 06 Jan 2017 14:46:51:  26000000 
INFO  @ Fri, 06 Jan 2017 14:46:59:  27000000 
INFO  @ Fri, 06 Jan 2017 14:47:07:  28000000 
INFO  @ Fri, 06 Jan 2017 14:47:15:  29000000 
INFO  @ Fri, 06 Jan 2017 14:47:24:  30000000 
INFO  @ Fri, 06 Jan 2017 14:47:32:  31000000 
INFO  @ Fri, 06 Jan 2017 14:47:40:  32000000 
INFO  @ Fri, 06 Jan 2017 14:47:48:  33000000 
INFO  @ Fri, 06 Jan 2017 14:47:56:  34000000 
INFO  @ Fri, 06 Jan 2017 14:48:03:  35000000 
INFO  @ Fri, 06 Jan 2017 14:48:11:  36000000 
INFO  @ Fri, 06 Jan 2017 14:48:19:  37000000 
INFO  @ Fri, 06 Jan 2017 14:48:27:  38000000 
INFO  @ Fri, 06 Jan 2017 14:48:34:  39000000 
INFO  @ Fri, 06 Jan 2017 14:48:42:  40000000 
INFO  @ Fri, 06 Jan 2017 14:48:49:  41000000 
INFO  @ Fri, 06 Jan 2017 14:48:57:  42000000 
INFO  @ Fri, 06 Jan 2017 14:49:04:  43000000 
INFO  @ Fri, 06 Jan 2017 14:49:12:  44000000 
INFO  @ Fri, 06 Jan 2017 14:49:20:  45000000 
INFO  @ Fri, 06 Jan 2017 14:49:28:  46000000 
INFO  @ Fri, 06 Jan 2017 14:49:36:  47000000 
INFO  @ Fri, 06 Jan 2017 14:49:43:  48000000 
INFO  @ Fri, 06 Jan 2017 14:49:50:  49000000 
INFO  @ Fri, 06 Jan 2017 14:49:58:  50000000 
INFO  @ Fri, 06 Jan 2017 14:50:02: #1 tag size is determined as 67 bps 
INFO  @ Fri, 06 Jan 2017 14:50:02: #1 tag size = 67 
INFO  @ Fri, 06 Jan 2017 14:50:02: #1  total tags in treatment: 15924789 
INFO  @ Fri, 06 Jan 2017 14:50:02: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:50:02: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:50:02: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:50:02: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:50:02: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:50:02: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:50:02: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:50:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:59:37: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:59:37: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:59:37: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:59:37: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:59:37: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:20:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:20:27: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:20:29: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:20:29: Done! 
INFO  @ Fri, 06 Jan 2017 15:20:37: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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 15:20:37: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:20:37: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:20:45:  1000000 
INFO  @ Fri, 06 Jan 2017 15:20:52:  2000000 
INFO  @ Fri, 06 Jan 2017 15:21:00:  3000000 
INFO  @ Fri, 06 Jan 2017 15:21:08:  4000000 
INFO  @ Fri, 06 Jan 2017 15:21:15:  5000000 
INFO  @ Fri, 06 Jan 2017 15:21:23:  6000000 
INFO  @ Fri, 06 Jan 2017 15:21:31:  7000000 
INFO  @ Fri, 06 Jan 2017 15:21:39:  8000000 
INFO  @ Fri, 06 Jan 2017 15:21:47:  9000000 
INFO  @ Fri, 06 Jan 2017 15:21:55:  10000000 
INFO  @ Fri, 06 Jan 2017 15:22:03:  11000000 
INFO  @ Fri, 06 Jan 2017 15:22:11:  12000000 
INFO  @ Fri, 06 Jan 2017 15:22:20:  13000000 
INFO  @ Fri, 06 Jan 2017 15:22:28:  14000000 
INFO  @ Fri, 06 Jan 2017 15:22:35:  15000000 
INFO  @ Fri, 06 Jan 2017 15:22:43: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:22:51:  1000000 
INFO  @ Fri, 06 Jan 2017 15:22:59:  2000000 
INFO  @ Fri, 06 Jan 2017 15:23:07:  3000000 
INFO  @ Fri, 06 Jan 2017 15:23:15:  4000000 
INFO  @ Fri, 06 Jan 2017 15:23:23:  5000000 
INFO  @ Fri, 06 Jan 2017 15:23:31:  6000000 
INFO  @ Fri, 06 Jan 2017 15:23:39:  7000000 
INFO  @ Fri, 06 Jan 2017 15:23:47:  8000000 
INFO  @ Fri, 06 Jan 2017 15:23:55:  9000000 
INFO  @ Fri, 06 Jan 2017 15:24:03:  10000000 
INFO  @ Fri, 06 Jan 2017 15:24:11:  11000000 
INFO  @ Fri, 06 Jan 2017 15:24:19:  12000000 
INFO  @ Fri, 06 Jan 2017 15:24:28:  13000000 
INFO  @ Fri, 06 Jan 2017 15:24:36:  14000000 
INFO  @ Fri, 06 Jan 2017 15:24:44:  15000000 
INFO  @ Fri, 06 Jan 2017 15:24:53:  16000000 
INFO  @ Fri, 06 Jan 2017 15:25:01:  17000000 
INFO  @ Fri, 06 Jan 2017 15:25:10:  18000000 
INFO  @ Fri, 06 Jan 2017 15:25:18:  19000000 
INFO  @ Fri, 06 Jan 2017 15:25:26:  20000000 
INFO  @ Fri, 06 Jan 2017 15:25:34:  21000000 
INFO  @ Fri, 06 Jan 2017 15:25:42:  22000000 
INFO  @ Fri, 06 Jan 2017 15:25:50:  23000000 
INFO  @ Fri, 06 Jan 2017 15:25:58:  24000000 
INFO  @ Fri, 06 Jan 2017 15:26:06:  25000000 
INFO  @ Fri, 06 Jan 2017 15:26:14:  26000000 
INFO  @ Fri, 06 Jan 2017 15:26:22:  27000000 
INFO  @ Fri, 06 Jan 2017 15:26:30:  28000000 
INFO  @ Fri, 06 Jan 2017 15:26:39:  29000000 
INFO  @ Fri, 06 Jan 2017 15:26:47:  30000000 
INFO  @ Fri, 06 Jan 2017 15:26:55:  31000000 
INFO  @ Fri, 06 Jan 2017 15:27:03:  32000000 
INFO  @ Fri, 06 Jan 2017 15:27:11:  33000000 
INFO  @ Fri, 06 Jan 2017 15:27:19:  34000000 
INFO  @ Fri, 06 Jan 2017 15:27:27:  35000000 
INFO  @ Fri, 06 Jan 2017 15:27:35:  36000000 
INFO  @ Fri, 06 Jan 2017 15:27:43:  37000000 
INFO  @ Fri, 06 Jan 2017 15:27:52:  38000000 
INFO  @ Fri, 06 Jan 2017 15:28:00:  39000000 
INFO  @ Fri, 06 Jan 2017 15:28:08:  40000000 
INFO  @ Fri, 06 Jan 2017 15:28:16:  41000000 
INFO  @ Fri, 06 Jan 2017 15:28:24:  42000000 
INFO  @ Fri, 06 Jan 2017 15:28:32:  43000000 
INFO  @ Fri, 06 Jan 2017 15:28:41:  44000000 
INFO  @ Fri, 06 Jan 2017 15:28:48:  45000000 
INFO  @ Fri, 06 Jan 2017 15:28:56:  46000000 
INFO  @ Fri, 06 Jan 2017 15:29:04:  47000000 
INFO  @ Fri, 06 Jan 2017 15:29:12:  48000000 
INFO  @ Fri, 06 Jan 2017 15:29:21:  49000000 
INFO  @ Fri, 06 Jan 2017 15:29:29:  50000000 
INFO  @ Fri, 06 Jan 2017 15:29:33: #1 tag size is determined as 67 bps 
INFO  @ Fri, 06 Jan 2017 15:29:33: #1 tag size = 67 
INFO  @ Fri, 06 Jan 2017 15:29:33: #1  total tags in treatment: 15924789 
INFO  @ Fri, 06 Jan 2017 15:29:33: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:29:33: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:29:33: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:29:33: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:29:33: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:29:33: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:29:33: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:29:33: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:38:33: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:46:38: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:47:02: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:47:17: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:47:30: Done! 
INFO  @ Fri, 06 Jan 2017 15:48:03: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:50:28: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:58:12: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:00:44: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:23:08: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:32:52: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:49:26: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:51:47: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:59:25: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 17:02:07: Values in your input bedGraph files will be multiplied by 15.924789 ... 
INFO  @ Fri, 06 Jan 2017 17:25:18: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:27:31: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:39:37: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/rep1/SRR1370908_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	24287

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

Start	2017-01-06 14:41:12
End	2017-01-08 02:05:52
Elapsed	1 day 11:24:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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--------------------
37867 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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 150 
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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign.gz 
opened /tmp/24287.1.amd.q/Rtmp6GzQpE/SRR1370908_1.nodup.pr1.tagAlign94afc230694
done. read 7962395 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24287.1.amd.q/Rtmp6GzQpE/input15MReadsNSCLess1.05.50MSubsample.tagAlign94af37d93d14
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1009426 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.10494313109465 
Top 3 estimates for fragment length 150 
Window half size 235 
Phantom peak location 70 
Phantom peak Correlation 0.1030845 
Normalized Strand cross-correlation coefficient (NSC) 1.039632 
Relative Strand cross-correlation Coefficient (RSC) 1.867771 
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= 6.281165  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1592061  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000037 
Detected 169761 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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2107	2343	.	0	.	31.83155027421	-1	3.19649709889411	118

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2107	2343	.	0	.	31.83155027421	-1	3.19649709889411	118

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24288

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

Start	2017-01-06 14:41:13
End	2017-01-08 01:02:39
Elapsed	1 day 10:21:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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--------------------
38154 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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 150 
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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign.gz 
opened /tmp/24288.1.amd.q/RtmpLNmJhr/SRR1370908_1.nodup.pr2.tagAlign9589232aa6d
done. read 7962394 fragments
ChIP data read length 69 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24288.1.amd.q/RtmpLNmJhr/input15MReadsNSCLess1.05.50MSubsample.tagAlign95895afb415f
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1006643 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.104648438828598 
Top 3 estimates for fragment length 150 
Window half size 230 
Phantom peak location 70 
Phantom peak Correlation 0.102732 
Normalized Strand cross-correlation coefficient (NSC) 1.039579 
Relative Strand cross-correlation Coefficient (RSC) 1.92687 
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= 6.28149  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1591979  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000196 
Detected 167683 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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2576	2806	.	0	.	22.0616420978656	-1	3.69905685454767	115

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2576	2806	.	0	.	22.0616420978656	-1	3.69905685454767	115

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24289

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

Start	2017-01-06 14:41:14
End	2017-01-06 15:46:58
Elapsed	01:05:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_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--------------------
38153 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:41:44: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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 14:41:44: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:41:44: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:41:51:  1000000 
INFO  @ Fri, 06 Jan 2017 14:41:59:  2000000 
INFO  @ Fri, 06 Jan 2017 14:42:06:  3000000 
INFO  @ Fri, 06 Jan 2017 14:42:14:  4000000 
INFO  @ Fri, 06 Jan 2017 14:42:21:  5000000 
INFO  @ Fri, 06 Jan 2017 14:42:29:  6000000 
INFO  @ Fri, 06 Jan 2017 14:42:36:  7000000 
INFO  @ Fri, 06 Jan 2017 14:42:44: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:42:52:  1000000 
INFO  @ Fri, 06 Jan 2017 14:42:59:  2000000 
INFO  @ Fri, 06 Jan 2017 14:43:07:  3000000 
INFO  @ Fri, 06 Jan 2017 14:43:14:  4000000 
INFO  @ Fri, 06 Jan 2017 14:43:22:  5000000 
INFO  @ Fri, 06 Jan 2017 14:43:30:  6000000 
INFO  @ Fri, 06 Jan 2017 14:43:38:  7000000 
INFO  @ Fri, 06 Jan 2017 14:43:45:  8000000 
INFO  @ Fri, 06 Jan 2017 14:43:53:  9000000 
INFO  @ Fri, 06 Jan 2017 14:44:01:  10000000 
INFO  @ Fri, 06 Jan 2017 14:44:09:  11000000 
INFO  @ Fri, 06 Jan 2017 14:44:16:  12000000 
INFO  @ Fri, 06 Jan 2017 14:44:24:  13000000 
INFO  @ Fri, 06 Jan 2017 14:44:32:  14000000 
INFO  @ Fri, 06 Jan 2017 14:44:39:  15000000 
INFO  @ Fri, 06 Jan 2017 14:44:47:  16000000 
INFO  @ Fri, 06 Jan 2017 14:44:55:  17000000 
INFO  @ Fri, 06 Jan 2017 14:45:03:  18000000 
INFO  @ Fri, 06 Jan 2017 14:45:11:  19000000 
INFO  @ Fri, 06 Jan 2017 14:45:19:  20000000 
INFO  @ Fri, 06 Jan 2017 14:45:27:  21000000 
INFO  @ Fri, 06 Jan 2017 14:45:35:  22000000 
INFO  @ Fri, 06 Jan 2017 14:45:43:  23000000 
INFO  @ Fri, 06 Jan 2017 14:45:51:  24000000 
INFO  @ Fri, 06 Jan 2017 14:45:59:  25000000 
INFO  @ Fri, 06 Jan 2017 14:46:08:  26000000 
INFO  @ Fri, 06 Jan 2017 14:46:16:  27000000 
INFO  @ Fri, 06 Jan 2017 14:46:24:  28000000 
INFO  @ Fri, 06 Jan 2017 14:46:32:  29000000 
INFO  @ Fri, 06 Jan 2017 14:46:41:  30000000 
INFO  @ Fri, 06 Jan 2017 14:46:48:  31000000 
INFO  @ Fri, 06 Jan 2017 14:46:57:  32000000 
INFO  @ Fri, 06 Jan 2017 14:47:05:  33000000 
INFO  @ Fri, 06 Jan 2017 14:47:14:  34000000 
INFO  @ Fri, 06 Jan 2017 14:47:22:  35000000 
INFO  @ Fri, 06 Jan 2017 14:47:31:  36000000 
INFO  @ Fri, 06 Jan 2017 14:47:39:  37000000 
INFO  @ Fri, 06 Jan 2017 14:47:47:  38000000 
INFO  @ Fri, 06 Jan 2017 14:47:54:  39000000 
INFO  @ Fri, 06 Jan 2017 14:48:02:  40000000 
INFO  @ Fri, 06 Jan 2017 14:48:10:  41000000 
INFO  @ Fri, 06 Jan 2017 14:48:19:  42000000 
INFO  @ Fri, 06 Jan 2017 14:48:27:  43000000 
INFO  @ Fri, 06 Jan 2017 14:48:35:  44000000 
INFO  @ Fri, 06 Jan 2017 14:48:43:  45000000 
INFO  @ Fri, 06 Jan 2017 14:48:51:  46000000 
INFO  @ Fri, 06 Jan 2017 14:48:59:  47000000 
INFO  @ Fri, 06 Jan 2017 14:49:08:  48000000 
INFO  @ Fri, 06 Jan 2017 14:49:16:  49000000 
INFO  @ Fri, 06 Jan 2017 14:49:24:  50000000 
INFO  @ Fri, 06 Jan 2017 14:49:28: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 14:49:28: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 14:49:28: #1  total tags in treatment: 7962395 
INFO  @ Fri, 06 Jan 2017 14:49:28: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:49:28: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:49:28: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:49:28: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:49:28: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:49:28: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:49:28: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:49:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:58:45: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:58:45: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:58:45: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:58:45: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:58:45: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:17:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:17:23: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:17:25: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:17:27: Done! 
INFO  @ Fri, 06 Jan 2017 15:17:34: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr1/SRR1370908_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 15:17:34: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:17:34: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:17:43:  1000000 
INFO  @ Fri, 06 Jan 2017 15:17:51:  2000000 
INFO  @ Fri, 06 Jan 2017 15:17:59:  3000000 
INFO  @ Fri, 06 Jan 2017 15:18:08:  4000000 
INFO  @ Fri, 06 Jan 2017 15:18:16:  5000000 
INFO  @ Fri, 06 Jan 2017 15:18:24:  6000000 
INFO  @ Fri, 06 Jan 2017 15:18:32:  7000000 
INFO  @ Fri, 06 Jan 2017 15:18:41: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:18:49:  1000000 
INFO  @ Fri, 06 Jan 2017 15:18:57:  2000000 
INFO  @ Fri, 06 Jan 2017 15:19:05:  3000000 
INFO  @ Fri, 06 Jan 2017 15:19:13:  4000000 
INFO  @ Fri, 06 Jan 2017 15:19:22:  5000000 
INFO  @ Fri, 06 Jan 2017 15:19:30:  6000000 
INFO  @ Fri, 06 Jan 2017 15:19:38:  7000000 
INFO  @ Fri, 06 Jan 2017 15:19:46:  8000000 
INFO  @ Fri, 06 Jan 2017 15:19:54:  9000000 
INFO  @ Fri, 06 Jan 2017 15:20:02:  10000000 
INFO  @ Fri, 06 Jan 2017 15:20:10:  11000000 
INFO  @ Fri, 06 Jan 2017 15:20:18:  12000000 
INFO  @ Fri, 06 Jan 2017 15:20:26:  13000000 
INFO  @ Fri, 06 Jan 2017 15:20:34:  14000000 
INFO  @ Fri, 06 Jan 2017 15:20:42:  15000000 
INFO  @ Fri, 06 Jan 2017 15:20:50:  16000000 
INFO  @ Fri, 06 Jan 2017 15:20:59:  17000000 
INFO  @ Fri, 06 Jan 2017 15:21:07:  18000000 
INFO  @ Fri, 06 Jan 2017 15:21:16:  19000000 
INFO  @ Fri, 06 Jan 2017 15:21:24:  20000000 
INFO  @ Fri, 06 Jan 2017 15:21:33:  21000000 
INFO  @ Fri, 06 Jan 2017 15:21:41:  22000000 
INFO  @ Fri, 06 Jan 2017 15:21:50:  23000000 
INFO  @ Fri, 06 Jan 2017 15:21:59:  24000000 
INFO  @ Fri, 06 Jan 2017 15:22:07:  25000000 
INFO  @ Fri, 06 Jan 2017 15:22:15:  26000000 
INFO  @ Fri, 06 Jan 2017 15:22:23:  27000000 
INFO  @ Fri, 06 Jan 2017 15:22:31:  28000000 
INFO  @ Fri, 06 Jan 2017 15:22:39:  29000000 
INFO  @ Fri, 06 Jan 2017 15:22:48:  30000000 
INFO  @ Fri, 06 Jan 2017 15:22:56:  31000000 
INFO  @ Fri, 06 Jan 2017 15:23:05:  32000000 
INFO  @ Fri, 06 Jan 2017 15:23:13:  33000000 
INFO  @ Fri, 06 Jan 2017 15:23:21:  34000000 
INFO  @ Fri, 06 Jan 2017 15:23:29:  35000000 
INFO  @ Fri, 06 Jan 2017 15:23:37:  36000000 
INFO  @ Fri, 06 Jan 2017 15:23:46:  37000000 
INFO  @ Fri, 06 Jan 2017 15:23:54:  38000000 
INFO  @ Fri, 06 Jan 2017 15:24:02:  39000000 
INFO  @ Fri, 06 Jan 2017 15:24:10:  40000000 
INFO  @ Fri, 06 Jan 2017 15:24:18:  41000000 
INFO  @ Fri, 06 Jan 2017 15:24:26:  42000000 
INFO  @ Fri, 06 Jan 2017 15:24:34:  43000000 
INFO  @ Fri, 06 Jan 2017 15:24:42:  44000000 
INFO  @ Fri, 06 Jan 2017 15:24:50:  45000000 
INFO  @ Fri, 06 Jan 2017 15:24:58:  46000000 
INFO  @ Fri, 06 Jan 2017 15:25:07:  47000000 
INFO  @ Fri, 06 Jan 2017 15:25:15:  48000000 
INFO  @ Fri, 06 Jan 2017 15:25:23:  49000000 
INFO  @ Fri, 06 Jan 2017 15:25:31:  50000000 
INFO  @ Fri, 06 Jan 2017 15:25:35: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 15:25:35: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 15:25:35: #1  total tags in treatment: 7962395 
INFO  @ Fri, 06 Jan 2017 15:25:35: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:25:35: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:25:35: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:25:35: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:25:35: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:25:35: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:25:35: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:25:35: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:35:03: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:45:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:45:39: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:45:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:46:18: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24337

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

Start	2017-01-06 15:47:00
End	2017-01-06 16:06:28
Elapsed	00:19:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_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--------------------
10104 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:47:24: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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 15:47:24: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:47:24: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:47:26:  1000000 
INFO  @ Fri, 06 Jan 2017 15:47:28:  2000000 
INFO  @ Fri, 06 Jan 2017 15:47:29:  3000000 
INFO  @ Fri, 06 Jan 2017 15:47:31:  4000000 
INFO  @ Fri, 06 Jan 2017 15:47:32:  5000000 
INFO  @ Fri, 06 Jan 2017 15:47:34:  6000000 
INFO  @ Fri, 06 Jan 2017 15:47:36:  7000000 
INFO  @ Fri, 06 Jan 2017 15:47:38: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:47:40:  1000000 
INFO  @ Fri, 06 Jan 2017 15:47:42:  2000000 
INFO  @ Fri, 06 Jan 2017 15:47:43:  3000000 
INFO  @ Fri, 06 Jan 2017 15:47:45:  4000000 
INFO  @ Fri, 06 Jan 2017 15:47:46:  5000000 
INFO  @ Fri, 06 Jan 2017 15:47:48:  6000000 
INFO  @ Fri, 06 Jan 2017 15:47:49:  7000000 
INFO  @ Fri, 06 Jan 2017 15:47:51:  8000000 
INFO  @ Fri, 06 Jan 2017 15:47:52:  9000000 
INFO  @ Fri, 06 Jan 2017 15:47:54:  10000000 
INFO  @ Fri, 06 Jan 2017 15:47:55:  11000000 
INFO  @ Fri, 06 Jan 2017 15:47:57:  12000000 
INFO  @ Fri, 06 Jan 2017 15:47:58:  13000000 
INFO  @ Fri, 06 Jan 2017 15:48:00:  14000000 
INFO  @ Fri, 06 Jan 2017 15:48:01:  15000000 
INFO  @ Fri, 06 Jan 2017 15:48:03:  16000000 
INFO  @ Fri, 06 Jan 2017 15:48:04:  17000000 
INFO  @ Fri, 06 Jan 2017 15:48:06:  18000000 
INFO  @ Fri, 06 Jan 2017 15:48:07:  19000000 
INFO  @ Fri, 06 Jan 2017 15:48:09:  20000000 
INFO  @ Fri, 06 Jan 2017 15:48:10:  21000000 
INFO  @ Fri, 06 Jan 2017 15:48:12:  22000000 
INFO  @ Fri, 06 Jan 2017 15:48:13:  23000000 
INFO  @ Fri, 06 Jan 2017 15:48:15:  24000000 
INFO  @ Fri, 06 Jan 2017 15:48:16:  25000000 
INFO  @ Fri, 06 Jan 2017 15:48:18:  26000000 
INFO  @ Fri, 06 Jan 2017 15:48:19:  27000000 
INFO  @ Fri, 06 Jan 2017 15:48:21:  28000000 
INFO  @ Fri, 06 Jan 2017 15:48:22:  29000000 
INFO  @ Fri, 06 Jan 2017 15:48:24:  30000000 
INFO  @ Fri, 06 Jan 2017 15:48:25:  31000000 
INFO  @ Fri, 06 Jan 2017 15:48:27:  32000000 
INFO  @ Fri, 06 Jan 2017 15:48:28:  33000000 
INFO  @ Fri, 06 Jan 2017 15:48:30:  34000000 
INFO  @ Fri, 06 Jan 2017 15:48:31:  35000000 
INFO  @ Fri, 06 Jan 2017 15:48:33:  36000000 
INFO  @ Fri, 06 Jan 2017 15:48:34:  37000000 
INFO  @ Fri, 06 Jan 2017 15:48:36:  38000000 
INFO  @ Fri, 06 Jan 2017 15:48:37:  39000000 
INFO  @ Fri, 06 Jan 2017 15:48:39:  40000000 
INFO  @ Fri, 06 Jan 2017 15:48:40:  41000000 
INFO  @ Fri, 06 Jan 2017 15:48:42:  42000000 
INFO  @ Fri, 06 Jan 2017 15:48:43:  43000000 
INFO  @ Fri, 06 Jan 2017 15:48:45:  44000000 
INFO  @ Fri, 06 Jan 2017 15:48:46:  45000000 
INFO  @ Fri, 06 Jan 2017 15:48:48:  46000000 
INFO  @ Fri, 06 Jan 2017 15:48:49:  47000000 
INFO  @ Fri, 06 Jan 2017 15:48:51:  48000000 
INFO  @ Fri, 06 Jan 2017 15:48:52:  49000000 
INFO  @ Fri, 06 Jan 2017 15:48:54:  50000000 
INFO  @ Fri, 06 Jan 2017 15:48:55: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 15:48:55: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 15:48:55: #1  total tags in treatment: 7962394 
INFO  @ Fri, 06 Jan 2017 15:48:55: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:48:55: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:48:55: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:48:55: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:48:55: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:48:55: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:48:55: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:48:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:52:00: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:52:00: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:52:00: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:52:00: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:52:00: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:57:09: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:57:10: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:57:11: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:57:11: Done! 
INFO  @ Fri, 06 Jan 2017 15:57:14: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/pseudo_reps/rep1/pr2/SRR1370908_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 15:57:14: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:57:14: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:57:16:  1000000 
INFO  @ Fri, 06 Jan 2017 15:57:19:  2000000 
INFO  @ Fri, 06 Jan 2017 15:57:21:  3000000 
INFO  @ Fri, 06 Jan 2017 15:57:23:  4000000 
INFO  @ Fri, 06 Jan 2017 15:57:24:  5000000 
INFO  @ Fri, 06 Jan 2017 15:57:26:  6000000 
INFO  @ Fri, 06 Jan 2017 15:57:29:  7000000 
INFO  @ Fri, 06 Jan 2017 15:57:32: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:57:35:  1000000 
INFO  @ Fri, 06 Jan 2017 15:57:37:  2000000 
INFO  @ Fri, 06 Jan 2017 15:57:38:  3000000 
INFO  @ Fri, 06 Jan 2017 15:57:40:  4000000 
INFO  @ Fri, 06 Jan 2017 15:57:42:  5000000 
INFO  @ Fri, 06 Jan 2017 15:57:44:  6000000 
INFO  @ Fri, 06 Jan 2017 15:57:46:  7000000 
INFO  @ Fri, 06 Jan 2017 15:57:47:  8000000 
INFO  @ Fri, 06 Jan 2017 15:57:49:  9000000 
INFO  @ Fri, 06 Jan 2017 15:57:51:  10000000 
INFO  @ Fri, 06 Jan 2017 15:57:53:  11000000 
INFO  @ Fri, 06 Jan 2017 15:57:55:  12000000 
INFO  @ Fri, 06 Jan 2017 15:57:57:  13000000 
INFO  @ Fri, 06 Jan 2017 15:57:58:  14000000 
INFO  @ Fri, 06 Jan 2017 15:58:01:  15000000 
INFO  @ Fri, 06 Jan 2017 15:58:03:  16000000 
INFO  @ Fri, 06 Jan 2017 15:58:06:  17000000 
INFO  @ Fri, 06 Jan 2017 15:58:08:  18000000 
INFO  @ Fri, 06 Jan 2017 15:58:10:  19000000 
INFO  @ Fri, 06 Jan 2017 15:58:12:  20000000 
INFO  @ Fri, 06 Jan 2017 15:58:14:  21000000 
INFO  @ Fri, 06 Jan 2017 15:58:16:  22000000 
INFO  @ Fri, 06 Jan 2017 15:58:18:  23000000 
INFO  @ Fri, 06 Jan 2017 15:58:20:  24000000 
INFO  @ Fri, 06 Jan 2017 15:58:21:  25000000 
INFO  @ Fri, 06 Jan 2017 15:58:23:  26000000 
INFO  @ Fri, 06 Jan 2017 15:58:26:  27000000 
INFO  @ Fri, 06 Jan 2017 15:58:28:  28000000 
INFO  @ Fri, 06 Jan 2017 15:58:30:  29000000 
INFO  @ Fri, 06 Jan 2017 15:58:31:  30000000 
INFO  @ Fri, 06 Jan 2017 15:58:33:  31000000 
INFO  @ Fri, 06 Jan 2017 15:58:35:  32000000 
INFO  @ Fri, 06 Jan 2017 15:58:37:  33000000 
INFO  @ Fri, 06 Jan 2017 15:58:39:  34000000 
INFO  @ Fri, 06 Jan 2017 15:58:40:  35000000 
INFO  @ Fri, 06 Jan 2017 15:58:42:  36000000 
INFO  @ Fri, 06 Jan 2017 15:58:44:  37000000 
INFO  @ Fri, 06 Jan 2017 15:58:46:  38000000 
INFO  @ Fri, 06 Jan 2017 15:58:48:  39000000 
INFO  @ Fri, 06 Jan 2017 15:58:50:  40000000 
INFO  @ Fri, 06 Jan 2017 15:58:52:  41000000 
INFO  @ Fri, 06 Jan 2017 15:58:54:  42000000 
INFO  @ Fri, 06 Jan 2017 15:58:57:  43000000 
INFO  @ Fri, 06 Jan 2017 15:58:59:  44000000 
INFO  @ Fri, 06 Jan 2017 15:59:00:  45000000 
INFO  @ Fri, 06 Jan 2017 15:59:02:  46000000 
INFO  @ Fri, 06 Jan 2017 15:59:03:  47000000 
INFO  @ Fri, 06 Jan 2017 15:59:05:  48000000 
INFO  @ Fri, 06 Jan 2017 15:59:06:  49000000 
INFO  @ Fri, 06 Jan 2017 15:59:08:  50000000 
INFO  @ Fri, 06 Jan 2017 15:59:10: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 15:59:10: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 15:59:10: #1  total tags in treatment: 7962394 
INFO  @ Fri, 06 Jan 2017 15:59:10: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:59:10: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:59:10: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:59:10: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:59:10: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:59:10: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:59:10: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:59:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:02:40: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:05:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:05:58: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:06:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:06:10: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24409

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

Start	2017-01-08 04:27:11
End	2017-01-08 04:28:23
Elapsed	00:01:11
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_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--------------------
47806 (process ID) old priority 0, new priority 10
Waiting for 58 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2107	2343	.	0	.	31.83155027421	-1	3.19649709889411	118

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2107	2343	.	0	.	31.83155027421	-1	3.19649709889411	118

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2576	2806	.	0	.	22.0616420978656	-1	3.69905685454767	115

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2576	2806	.	0	.	22.0616420978656	-1	3.69905685454767	115

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000205.2	33624	33848	.	0	.	3.98208933624708	-1	1.62600205462958	112

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000205.2	33624	33848	.	0	.	3.98208933624708	-1	1.62600205462958	112

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24410

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

Start	2017-01-08 04:28:25
End	2017-01-08 04:29:38
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370908_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370908_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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--------------------
47912 (process ID) old priority 0, new priority 10
Waiting for 17 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.73 1.29 0.84 0.23]
Number of reported peaks - 12663/12663 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 1636/12663 (12.9%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24411

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

Start	2017-01-08 04:29:39
End	2017-01-08 04:30:53
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/qc/ZNF454_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/ZNF454/out/qc/ZNF454_IDR_final.qc

# SYS command. line 224

 echo -e "0\t37	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/qc/ZNF454_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--------------------
48063 (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	3801

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

Start	2017-01-08 04:30:55
End	2017-01-08 04:32:03
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_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/ZNF454/out/peak/spp/rep1/SRR1370908_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--------------------
3805 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2581	2805	.	0	.	46.5875372222257	-1	3.67860941655892	112

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/rep1/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2581	2805	.	0	.	46.5875372222257	-1	3.67860941655892	112

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	7585

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

Start	2017-01-08 04:32:04
End	2017-01-08 04:32:13
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/spp/overlap/SRR1370908_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/ZNF454/out/peak/spp/overlap/SRR1370908_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
7589 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	8175

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

Start	2017-01-08 04:32:14
End	2017-01-08 04:32:22
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_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/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/peak/idr/pseudo_reps/rep1/ZNF454_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
8179 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	8750

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

Start	2017-01-08 04:32:23
End	2017-01-08 04:32:31
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/ZNF454/out/report/ZNF454_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/report/ZNF454_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/report/ZNF454_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
8754 (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, ZNF454, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF454/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF454/out/align/rep1/SRR1370908_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/ZNF454
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/ZNF454
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	12131.ZNF454.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