Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_143435_638
Start time	2017-01-06 14:34:35
Run time	1 day 05:23:23.940
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF264, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF264/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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_143435_638/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_143435_638/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_143435_638/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_143435_638/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_143435_638/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_143435_638/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_143435_638/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_143435_638/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_143435_638/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_143435_638/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_143435_638/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_143435_638/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_143435_638/task.graphviz.report.line_97.id_24
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_spp.spp_rep1.line_57.id_10
Name	spp rep1
Thread	thread_Root
PID	24256

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

Start	2017-01-06 14:34:42
End	2017-01-07 19:52:41
Elapsed	1 day 05:17:59
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_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--------------------
34686 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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 145 
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/ZNF264/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/align/rep1/SRR1370899_1.nodup.tagAlign.gz 
opened /tmp/24256.1.amd.q/RtmpPTMVHF/SRR1370899_1.nodup.tagAlign883b6c4b368a
done. read 14679478 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/24256.1.amd.q/RtmpPTMVHF/input15MReadsNSCLess1.05.50MSubsample.tagAlign883bae26a57
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.170506 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.188589906978053 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.1746544 
Normalized Strand cross-correlation coefficient (NSC) 1.10606 
Relative Strand cross-correlation Coefficient (RSC) 4.359293 
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= 3.412625  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2930296  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000255 
Detected 499853 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/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	42707	42784	.	0	.	49.4743803912797	-1	3.60863298949003	29

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	42707	42784	.	0	.	49.4743803912797	-1	3.60863298949003	29

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24257

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

Start	2017-01-06 14:34:42
End	2017-01-06 17:47:30
Elapsed	03:12:47
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/signal/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/signal/macs2/rep1/SRR1370899_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/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1 -o "SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/signal/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1 -o "SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/signal/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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--------------------
34685 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:35:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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 14:35:00: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:35:00: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:35:06:  1000000 
INFO  @ Fri, 06 Jan 2017 14:35:12:  2000000 
INFO  @ Fri, 06 Jan 2017 14:35:18:  3000000 
INFO  @ Fri, 06 Jan 2017 14:35:24:  4000000 
INFO  @ Fri, 06 Jan 2017 14:35:30:  5000000 
INFO  @ Fri, 06 Jan 2017 14:35:36:  6000000 
INFO  @ Fri, 06 Jan 2017 14:35:42:  7000000 
INFO  @ Fri, 06 Jan 2017 14:35:48:  8000000 
INFO  @ Fri, 06 Jan 2017 14:35:54:  9000000 
INFO  @ Fri, 06 Jan 2017 14:36:00:  10000000 
INFO  @ Fri, 06 Jan 2017 14:36:06:  11000000 
INFO  @ Fri, 06 Jan 2017 14:36:11:  12000000 
INFO  @ Fri, 06 Jan 2017 14:36:17:  13000000 
INFO  @ Fri, 06 Jan 2017 14:36:23:  14000000 
INFO  @ Fri, 06 Jan 2017 14:36:28: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:36:34:  1000000 
INFO  @ Fri, 06 Jan 2017 14:36:40:  2000000 
INFO  @ Fri, 06 Jan 2017 14:36:46:  3000000 
INFO  @ Fri, 06 Jan 2017 14:36:52:  4000000 
INFO  @ Fri, 06 Jan 2017 14:36:58:  5000000 
INFO  @ Fri, 06 Jan 2017 14:37:04:  6000000 
INFO  @ Fri, 06 Jan 2017 14:37:10:  7000000 
INFO  @ Fri, 06 Jan 2017 14:37:16:  8000000 
INFO  @ Fri, 06 Jan 2017 14:37:22:  9000000 
INFO  @ Fri, 06 Jan 2017 14:37:28:  10000000 
INFO  @ Fri, 06 Jan 2017 14:37:34:  11000000 
INFO  @ Fri, 06 Jan 2017 14:37:41:  12000000 
INFO  @ Fri, 06 Jan 2017 14:37:47:  13000000 
INFO  @ Fri, 06 Jan 2017 14:37:53:  14000000 
INFO  @ Fri, 06 Jan 2017 14:37:59:  15000000 
INFO  @ Fri, 06 Jan 2017 14:38:05:  16000000 
INFO  @ Fri, 06 Jan 2017 14:38:12:  17000000 
INFO  @ Fri, 06 Jan 2017 14:38:18:  18000000 
INFO  @ Fri, 06 Jan 2017 14:38:24:  19000000 
INFO  @ Fri, 06 Jan 2017 14:38:31:  20000000 
INFO  @ Fri, 06 Jan 2017 14:38:38:  21000000 
INFO  @ Fri, 06 Jan 2017 14:38:44:  22000000 
INFO  @ Fri, 06 Jan 2017 14:38:51:  23000000 
INFO  @ Fri, 06 Jan 2017 14:38:57:  24000000 
INFO  @ Fri, 06 Jan 2017 14:39:04:  25000000 
INFO  @ Fri, 06 Jan 2017 14:39:10:  26000000 
INFO  @ Fri, 06 Jan 2017 14:39:17:  27000000 
INFO  @ Fri, 06 Jan 2017 14:39:23:  28000000 
INFO  @ Fri, 06 Jan 2017 14:39:30:  29000000 
INFO  @ Fri, 06 Jan 2017 14:39:36:  30000000 
INFO  @ Fri, 06 Jan 2017 14:39:43:  31000000 
INFO  @ Fri, 06 Jan 2017 14:39:49:  32000000 
INFO  @ Fri, 06 Jan 2017 14:39:56:  33000000 
INFO  @ Fri, 06 Jan 2017 14:40:03:  34000000 
INFO  @ Fri, 06 Jan 2017 14:40:09:  35000000 
INFO  @ Fri, 06 Jan 2017 14:40:16:  36000000 
INFO  @ Fri, 06 Jan 2017 14:40:23:  37000000 
INFO  @ Fri, 06 Jan 2017 14:40:30:  38000000 
INFO  @ Fri, 06 Jan 2017 14:40:37:  39000000 
INFO  @ Fri, 06 Jan 2017 14:40:43:  40000000 
INFO  @ Fri, 06 Jan 2017 14:40:50:  41000000 
INFO  @ Fri, 06 Jan 2017 14:40:56:  42000000 
INFO  @ Fri, 06 Jan 2017 14:41:03:  43000000 
INFO  @ Fri, 06 Jan 2017 14:41:10:  44000000 
INFO  @ Fri, 06 Jan 2017 14:41:16:  45000000 
INFO  @ Fri, 06 Jan 2017 14:41:23:  46000000 
INFO  @ Fri, 06 Jan 2017 14:41:30:  47000000 
INFO  @ Fri, 06 Jan 2017 14:41:37:  48000000 
INFO  @ Fri, 06 Jan 2017 14:41:44:  49000000 
INFO  @ Fri, 06 Jan 2017 14:41:51:  50000000 
INFO  @ Fri, 06 Jan 2017 14:41:55: #1 tag size is determined as 68 bps 
INFO  @ Fri, 06 Jan 2017 14:41:55: #1 tag size = 68 
INFO  @ Fri, 06 Jan 2017 14:41:55: #1  total tags in treatment: 14679478 
INFO  @ Fri, 06 Jan 2017 14:41:55: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:41:55: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:41:55: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:41:55: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:41:55: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:41:55: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:41:55: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:41:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:50:53: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:50:53: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:50:53: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:50:53: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:50:53: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:10:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:11:00: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:11:03: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:11:06: Done! 
INFO  @ Fri, 06 Jan 2017 15:11:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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 15:11:16: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:11:16: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:11:25:  1000000 
INFO  @ Fri, 06 Jan 2017 15:11:34:  2000000 
INFO  @ Fri, 06 Jan 2017 15:11:42:  3000000 
INFO  @ Fri, 06 Jan 2017 15:11:50:  4000000 
INFO  @ Fri, 06 Jan 2017 15:11:58:  5000000 
INFO  @ Fri, 06 Jan 2017 15:12:06:  6000000 
INFO  @ Fri, 06 Jan 2017 15:12:14:  7000000 
INFO  @ Fri, 06 Jan 2017 15:12:21:  8000000 
INFO  @ Fri, 06 Jan 2017 15:12:29:  9000000 
INFO  @ Fri, 06 Jan 2017 15:12:37:  10000000 
INFO  @ Fri, 06 Jan 2017 15:12:44:  11000000 
INFO  @ Fri, 06 Jan 2017 15:12:52:  12000000 
INFO  @ Fri, 06 Jan 2017 15:12:59:  13000000 
INFO  @ Fri, 06 Jan 2017 15:13:07:  14000000 
INFO  @ Fri, 06 Jan 2017 15:13:13: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:13:21:  1000000 
INFO  @ Fri, 06 Jan 2017 15:13:29:  2000000 
INFO  @ Fri, 06 Jan 2017 15:13:37:  3000000 
INFO  @ Fri, 06 Jan 2017 15:13:45:  4000000 
INFO  @ Fri, 06 Jan 2017 15:13:52:  5000000 
INFO  @ Fri, 06 Jan 2017 15:14:00:  6000000 
INFO  @ Fri, 06 Jan 2017 15:14:07:  7000000 
INFO  @ Fri, 06 Jan 2017 15:14:15:  8000000 
INFO  @ Fri, 06 Jan 2017 15:14:23:  9000000 
INFO  @ Fri, 06 Jan 2017 15:14:30:  10000000 
INFO  @ Fri, 06 Jan 2017 15:14:38:  11000000 
INFO  @ Fri, 06 Jan 2017 15:14:48:  12000000 
INFO  @ Fri, 06 Jan 2017 15:14:57:  13000000 
INFO  @ Fri, 06 Jan 2017 15:15:07:  14000000 
INFO  @ Fri, 06 Jan 2017 15:15:16:  15000000 
INFO  @ Fri, 06 Jan 2017 15:15:26:  16000000 
INFO  @ Fri, 06 Jan 2017 15:15:35:  17000000 
INFO  @ Fri, 06 Jan 2017 15:15:45:  18000000 
INFO  @ Fri, 06 Jan 2017 15:15:54:  19000000 
INFO  @ Fri, 06 Jan 2017 15:16:04:  20000000 
INFO  @ Fri, 06 Jan 2017 15:16:13:  21000000 
INFO  @ Fri, 06 Jan 2017 15:16:22:  22000000 
INFO  @ Fri, 06 Jan 2017 15:16:29:  23000000 
INFO  @ Fri, 06 Jan 2017 15:16:37:  24000000 
INFO  @ Fri, 06 Jan 2017 15:16:45:  25000000 
INFO  @ Fri, 06 Jan 2017 15:16:53:  26000000 
INFO  @ Fri, 06 Jan 2017 15:17:00:  27000000 
INFO  @ Fri, 06 Jan 2017 15:17:08:  28000000 
INFO  @ Fri, 06 Jan 2017 15:17:16:  29000000 
INFO  @ Fri, 06 Jan 2017 15:17:24:  30000000 
INFO  @ Fri, 06 Jan 2017 15:17:31:  31000000 
INFO  @ Fri, 06 Jan 2017 15:17:39:  32000000 
INFO  @ Fri, 06 Jan 2017 15:17:47:  33000000 
INFO  @ Fri, 06 Jan 2017 15:17:55:  34000000 
INFO  @ Fri, 06 Jan 2017 15:18:03:  35000000 
INFO  @ Fri, 06 Jan 2017 15:18:11:  36000000 
INFO  @ Fri, 06 Jan 2017 15:18:18:  37000000 
INFO  @ Fri, 06 Jan 2017 15:18:26:  38000000 
INFO  @ Fri, 06 Jan 2017 15:18:34:  39000000 
INFO  @ Fri, 06 Jan 2017 15:18:42:  40000000 
INFO  @ Fri, 06 Jan 2017 15:18:50:  41000000 
INFO  @ Fri, 06 Jan 2017 15:18:58:  42000000 
INFO  @ Fri, 06 Jan 2017 15:19:06:  43000000 
INFO  @ Fri, 06 Jan 2017 15:19:14:  44000000 
INFO  @ Fri, 06 Jan 2017 15:19:21:  45000000 
INFO  @ Fri, 06 Jan 2017 15:19:29:  46000000 
INFO  @ Fri, 06 Jan 2017 15:19:37:  47000000 
INFO  @ Fri, 06 Jan 2017 15:19:45:  48000000 
INFO  @ Fri, 06 Jan 2017 15:19:52:  49000000 
INFO  @ Fri, 06 Jan 2017 15:20:00:  50000000 
INFO  @ Fri, 06 Jan 2017 15:20:04: #1 tag size is determined as 68 bps 
INFO  @ Fri, 06 Jan 2017 15:20:04: #1 tag size = 68 
INFO  @ Fri, 06 Jan 2017 15:20:04: #1  total tags in treatment: 14679478 
INFO  @ Fri, 06 Jan 2017 15:20:04: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:20:04: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:20:04: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:20:04: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:20:04: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:20:04: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:20:04: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:20:04: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:28:48: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:37:32: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:37:56: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:38:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:38:27: Done! 
INFO  @ Fri, 06 Jan 2017 15:39:06: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:41:19: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:49:11: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:51:52: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:14:48: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:23:47: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:39:32: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:41:36: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:49:06: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:51:52: Values in your input bedGraph files will be multiplied by 14.679478 ... 
INFO  @ Fri, 06 Jan 2017 17:13:36: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:15:40: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:26:37: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/rep1/SRR1370899_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	24258

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

Start	2017-01-06 14:34:43
End	2017-01-07 17:23:22
Elapsed	1 day 02:48:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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--------------------
34905 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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 145 
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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign.gz 
opened /tmp/24258.1.amd.q/RtmpV1WNCA/SRR1370899_1.nodup.pr1.tagAlign89146edb0960
done. read 7339739 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/24258.1.amd.q/RtmpV1WNCA/input15MReadsNSCLess1.05.50MSubsample.tagAlign89145117e819
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.09380055 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.103717004428745 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.09611246 
Normalized Strand cross-correlation coefficient (NSC) 1.105719 
Relative Strand cross-correlation Coefficient (RSC) 4.289278 
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= 6.818265  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1466649  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000248 
Detected 169923 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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	42646	42826	.	0	.	24.8190531804466	-1	3.7610144953249	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	42646	42826	.	0	.	24.8190531804466	-1	3.7610144953249	90

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24259

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

Start	2017-01-06 14:34:44
End	2017-01-07 17:04:56
Elapsed	1 day 02:30:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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--------------------
34907 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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 145 
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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign.gz 
opened /tmp/24259.1.amd.q/RtmpWzcDuz/SRR1370899_1.nodup.pr2.tagAlign891f1533f22e
done. read 7339739 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/24259.1.amd.q/RtmpWzcDuz/input15MReadsNSCLess1.05.50MSubsample.tagAlign891f45433c4
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.09361811 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.103487482679613 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 70 
Phantom peak Correlation 0.09594705 
Normalized Strand cross-correlation coefficient (NSC) 1.105422 
Relative Strand cross-correlation Coefficient (RSC) 4.237712 
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= 6.817966  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1466713  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00023 
Detected 169080 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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2564	2744	.	0	.	31.5554888252011	-1	3.59194600653173	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196487.1	2564	2744	.	0	.	31.5554888252011	-1	3.59194600653173	90

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24260

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

Start	2017-01-06 14:34:45
End	2017-01-06 15:39:09
Elapsed	01:04:23
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_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--------------------
34906 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:35:14: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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 14:35:14: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:35:14: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:35:21:  1000000 
INFO  @ Fri, 06 Jan 2017 14:35:27:  2000000 
INFO  @ Fri, 06 Jan 2017 14:35:33:  3000000 
INFO  @ Fri, 06 Jan 2017 14:35:39:  4000000 
INFO  @ Fri, 06 Jan 2017 14:35:45:  5000000 
INFO  @ Fri, 06 Jan 2017 14:35:52:  6000000 
INFO  @ Fri, 06 Jan 2017 14:35:58:  7000000 
INFO  @ Fri, 06 Jan 2017 14:36:01: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:36:07:  1000000 
INFO  @ Fri, 06 Jan 2017 14:36:13:  2000000 
INFO  @ Fri, 06 Jan 2017 14:36:19:  3000000 
INFO  @ Fri, 06 Jan 2017 14:36:25:  4000000 
INFO  @ Fri, 06 Jan 2017 14:36:31:  5000000 
INFO  @ Fri, 06 Jan 2017 14:36:37:  6000000 
INFO  @ Fri, 06 Jan 2017 14:36:43:  7000000 
INFO  @ Fri, 06 Jan 2017 14:36:49:  8000000 
INFO  @ Fri, 06 Jan 2017 14:36:56:  9000000 
INFO  @ Fri, 06 Jan 2017 14:37:02:  10000000 
INFO  @ Fri, 06 Jan 2017 14:37:08:  11000000 
INFO  @ Fri, 06 Jan 2017 14:37:14:  12000000 
INFO  @ Fri, 06 Jan 2017 14:37:20:  13000000 
INFO  @ Fri, 06 Jan 2017 14:37:26:  14000000 
INFO  @ Fri, 06 Jan 2017 14:37:33:  15000000 
INFO  @ Fri, 06 Jan 2017 14:37:39:  16000000 
INFO  @ Fri, 06 Jan 2017 14:37:45:  17000000 
INFO  @ Fri, 06 Jan 2017 14:37:51:  18000000 
INFO  @ Fri, 06 Jan 2017 14:37:57:  19000000 
INFO  @ Fri, 06 Jan 2017 14:38:04:  20000000 
INFO  @ Fri, 06 Jan 2017 14:38:10:  21000000 
INFO  @ Fri, 06 Jan 2017 14:38:16:  22000000 
INFO  @ Fri, 06 Jan 2017 14:38:23:  23000000 
INFO  @ Fri, 06 Jan 2017 14:38:29:  24000000 
INFO  @ Fri, 06 Jan 2017 14:38:36:  25000000 
INFO  @ Fri, 06 Jan 2017 14:38:42:  26000000 
INFO  @ Fri, 06 Jan 2017 14:38:49:  27000000 
INFO  @ Fri, 06 Jan 2017 14:38:55:  28000000 
INFO  @ Fri, 06 Jan 2017 14:39:01:  29000000 
INFO  @ Fri, 06 Jan 2017 14:39:08:  30000000 
INFO  @ Fri, 06 Jan 2017 14:39:14:  31000000 
INFO  @ Fri, 06 Jan 2017 14:39:20:  32000000 
INFO  @ Fri, 06 Jan 2017 14:39:27:  33000000 
INFO  @ Fri, 06 Jan 2017 14:39:33:  34000000 
INFO  @ Fri, 06 Jan 2017 14:39:40:  35000000 
INFO  @ Fri, 06 Jan 2017 14:39:46:  36000000 
INFO  @ Fri, 06 Jan 2017 14:39:52:  37000000 
INFO  @ Fri, 06 Jan 2017 14:39:59:  38000000 
INFO  @ Fri, 06 Jan 2017 14:40:05:  39000000 
INFO  @ Fri, 06 Jan 2017 14:40:12:  40000000 
INFO  @ Fri, 06 Jan 2017 14:40:19:  41000000 
INFO  @ Fri, 06 Jan 2017 14:40:25:  42000000 
INFO  @ Fri, 06 Jan 2017 14:40:32:  43000000 
INFO  @ Fri, 06 Jan 2017 14:40:39:  44000000 
INFO  @ Fri, 06 Jan 2017 14:40:47:  45000000 
INFO  @ Fri, 06 Jan 2017 14:40:55:  46000000 
INFO  @ Fri, 06 Jan 2017 14:41:02:  47000000 
INFO  @ Fri, 06 Jan 2017 14:41:09:  48000000 
INFO  @ Fri, 06 Jan 2017 14:41:16:  49000000 
INFO  @ Fri, 06 Jan 2017 14:41:23:  50000000 
INFO  @ Fri, 06 Jan 2017 14:41:27: #1 tag size is determined as 68 bps 
INFO  @ Fri, 06 Jan 2017 14:41:27: #1 tag size = 68 
INFO  @ Fri, 06 Jan 2017 14:41:27: #1  total tags in treatment: 7339739 
INFO  @ Fri, 06 Jan 2017 14:41:27: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:41:27: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:41:27: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:41:27: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:41:27: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:41:27: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:41:27: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:41:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:50:49: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:50:49: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:50:49: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:50:49: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:50:49: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:10:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:11:05: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:11:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:11:11: Done! 
INFO  @ Fri, 06 Jan 2017 15:11:19: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr1/SRR1370899_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 15:11:19: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:11:19: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:11:28:  1000000 
INFO  @ Fri, 06 Jan 2017 15:11:36:  2000000 
INFO  @ Fri, 06 Jan 2017 15:11:44:  3000000 
INFO  @ Fri, 06 Jan 2017 15:11:52:  4000000 
INFO  @ Fri, 06 Jan 2017 15:12:00:  5000000 
INFO  @ Fri, 06 Jan 2017 15:12:07:  6000000 
INFO  @ Fri, 06 Jan 2017 15:12:15:  7000000 
INFO  @ Fri, 06 Jan 2017 15:12:19: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:12:28:  1000000 
INFO  @ Fri, 06 Jan 2017 15:12:36:  2000000 
INFO  @ Fri, 06 Jan 2017 15:12:43:  3000000 
INFO  @ Fri, 06 Jan 2017 15:12:51:  4000000 
INFO  @ Fri, 06 Jan 2017 15:12:59:  5000000 
INFO  @ Fri, 06 Jan 2017 15:13:08:  6000000 
INFO  @ Fri, 06 Jan 2017 15:13:15:  7000000 
INFO  @ Fri, 06 Jan 2017 15:13:22:  8000000 
INFO  @ Fri, 06 Jan 2017 15:13:30:  9000000 
INFO  @ Fri, 06 Jan 2017 15:13:38:  10000000 
INFO  @ Fri, 06 Jan 2017 15:13:45:  11000000 
INFO  @ Fri, 06 Jan 2017 15:13:53:  12000000 
INFO  @ Fri, 06 Jan 2017 15:14:00:  13000000 
INFO  @ Fri, 06 Jan 2017 15:14:08:  14000000 
INFO  @ Fri, 06 Jan 2017 15:14:15:  15000000 
INFO  @ Fri, 06 Jan 2017 15:14:23:  16000000 
INFO  @ Fri, 06 Jan 2017 15:14:30:  17000000 
INFO  @ Fri, 06 Jan 2017 15:14:38:  18000000 
INFO  @ Fri, 06 Jan 2017 15:14:46:  19000000 
INFO  @ Fri, 06 Jan 2017 15:14:53:  20000000 
INFO  @ Fri, 06 Jan 2017 15:15:01:  21000000 
INFO  @ Fri, 06 Jan 2017 15:15:08:  22000000 
INFO  @ Fri, 06 Jan 2017 15:15:16:  23000000 
INFO  @ Fri, 06 Jan 2017 15:15:23:  24000000 
INFO  @ Fri, 06 Jan 2017 15:15:30:  25000000 
INFO  @ Fri, 06 Jan 2017 15:15:37:  26000000 
INFO  @ Fri, 06 Jan 2017 15:15:45:  27000000 
INFO  @ Fri, 06 Jan 2017 15:15:52:  28000000 
INFO  @ Fri, 06 Jan 2017 15:15:59:  29000000 
INFO  @ Fri, 06 Jan 2017 15:16:06:  30000000 
INFO  @ Fri, 06 Jan 2017 15:16:14:  31000000 
INFO  @ Fri, 06 Jan 2017 15:16:21:  32000000 
INFO  @ Fri, 06 Jan 2017 15:16:28:  33000000 
INFO  @ Fri, 06 Jan 2017 15:16:36:  34000000 
INFO  @ Fri, 06 Jan 2017 15:16:44:  35000000 
INFO  @ Fri, 06 Jan 2017 15:16:52:  36000000 
INFO  @ Fri, 06 Jan 2017 15:16:59:  37000000 
INFO  @ Fri, 06 Jan 2017 15:17:07:  38000000 
INFO  @ Fri, 06 Jan 2017 15:17:14:  39000000 
INFO  @ Fri, 06 Jan 2017 15:17:21:  40000000 
INFO  @ Fri, 06 Jan 2017 15:17:28:  41000000 
INFO  @ Fri, 06 Jan 2017 15:17:36:  42000000 
INFO  @ Fri, 06 Jan 2017 15:17:43:  43000000 
INFO  @ Fri, 06 Jan 2017 15:17:50:  44000000 
INFO  @ Fri, 06 Jan 2017 15:17:57:  45000000 
INFO  @ Fri, 06 Jan 2017 15:18:05:  46000000 
INFO  @ Fri, 06 Jan 2017 15:18:13:  47000000 
INFO  @ Fri, 06 Jan 2017 15:18:20:  48000000 
INFO  @ Fri, 06 Jan 2017 15:18:28:  49000000 
INFO  @ Fri, 06 Jan 2017 15:18:36:  50000000 
INFO  @ Fri, 06 Jan 2017 15:18:40: #1 tag size is determined as 68 bps 
INFO  @ Fri, 06 Jan 2017 15:18:40: #1 tag size = 68 
INFO  @ Fri, 06 Jan 2017 15:18:40: #1  total tags in treatment: 7339739 
INFO  @ Fri, 06 Jan 2017 15:18:40: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:18:40: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:18:40: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:18:40: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:18:40: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:18:40: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:18:40: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:18:40: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:27:05: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:37:16: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:37:45: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:38:06: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:38:24: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24332

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

Start	2017-01-06 15:39:12
End	2017-01-06 16:38:27
Elapsed	00:59:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_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--------------------
42307 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:39:33: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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 15:39:33: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:39:33: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:39:42:  1000000 
INFO  @ Fri, 06 Jan 2017 15:39:51:  2000000 
INFO  @ Fri, 06 Jan 2017 15:40:00:  3000000 
INFO  @ Fri, 06 Jan 2017 15:40:09:  4000000 
INFO  @ Fri, 06 Jan 2017 15:40:17:  5000000 
INFO  @ Fri, 06 Jan 2017 15:40:26:  6000000 
INFO  @ Fri, 06 Jan 2017 15:40:35:  7000000 
INFO  @ Fri, 06 Jan 2017 15:40:38: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:40:46:  1000000 
INFO  @ Fri, 06 Jan 2017 15:40:54:  2000000 
INFO  @ Fri, 06 Jan 2017 15:41:02:  3000000 
INFO  @ Fri, 06 Jan 2017 15:41:11:  4000000 
INFO  @ Fri, 06 Jan 2017 15:41:19:  5000000 
INFO  @ Fri, 06 Jan 2017 15:41:27:  6000000 
INFO  @ Fri, 06 Jan 2017 15:41:35:  7000000 
INFO  @ Fri, 06 Jan 2017 15:41:42:  8000000 
INFO  @ Fri, 06 Jan 2017 15:41:50:  9000000 
INFO  @ Fri, 06 Jan 2017 15:41:58:  10000000 
INFO  @ Fri, 06 Jan 2017 15:42:05:  11000000 
INFO  @ Fri, 06 Jan 2017 15:42:13:  12000000 
INFO  @ Fri, 06 Jan 2017 15:42:21:  13000000 
INFO  @ Fri, 06 Jan 2017 15:42:30:  14000000 
INFO  @ Fri, 06 Jan 2017 15:42:38:  15000000 
INFO  @ Fri, 06 Jan 2017 15:42:46:  16000000 
INFO  @ Fri, 06 Jan 2017 15:42:55:  17000000 
INFO  @ Fri, 06 Jan 2017 15:43:03:  18000000 
INFO  @ Fri, 06 Jan 2017 15:43:10:  19000000 
INFO  @ Fri, 06 Jan 2017 15:43:18:  20000000 
INFO  @ Fri, 06 Jan 2017 15:43:26:  21000000 
INFO  @ Fri, 06 Jan 2017 15:43:33:  22000000 
INFO  @ Fri, 06 Jan 2017 15:43:41:  23000000 
INFO  @ Fri, 06 Jan 2017 15:43:48:  24000000 
INFO  @ Fri, 06 Jan 2017 15:43:56:  25000000 
INFO  @ Fri, 06 Jan 2017 15:44:04:  26000000 
INFO  @ Fri, 06 Jan 2017 15:44:11:  27000000 
INFO  @ Fri, 06 Jan 2017 15:44:18:  28000000 
INFO  @ Fri, 06 Jan 2017 15:44:26:  29000000 
INFO  @ Fri, 06 Jan 2017 15:44:33:  30000000 
INFO  @ Fri, 06 Jan 2017 15:44:41:  31000000 
INFO  @ Fri, 06 Jan 2017 15:44:49:  32000000 
INFO  @ Fri, 06 Jan 2017 15:44:56:  33000000 
INFO  @ Fri, 06 Jan 2017 15:45:04:  34000000 
INFO  @ Fri, 06 Jan 2017 15:45:11:  35000000 
INFO  @ Fri, 06 Jan 2017 15:45:19:  36000000 
INFO  @ Fri, 06 Jan 2017 15:45:27:  37000000 
INFO  @ Fri, 06 Jan 2017 15:45:35:  38000000 
INFO  @ Fri, 06 Jan 2017 15:45:43:  39000000 
INFO  @ Fri, 06 Jan 2017 15:45:52:  40000000 
INFO  @ Fri, 06 Jan 2017 15:46:00:  41000000 
INFO  @ Fri, 06 Jan 2017 15:46:08:  42000000 
INFO  @ Fri, 06 Jan 2017 15:46:16:  43000000 
INFO  @ Fri, 06 Jan 2017 15:46:24:  44000000 
INFO  @ Fri, 06 Jan 2017 15:46:32:  45000000 
INFO  @ Fri, 06 Jan 2017 15:46:40:  46000000 
INFO  @ Fri, 06 Jan 2017 15:46:48:  47000000 
INFO  @ Fri, 06 Jan 2017 15:46:55:  48000000 
INFO  @ Fri, 06 Jan 2017 15:47:03:  49000000 
INFO  @ Fri, 06 Jan 2017 15:47:11:  50000000 
INFO  @ Fri, 06 Jan 2017 15:47:14: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 15:47:14: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 15:47:14: #1  total tags in treatment: 7339739 
INFO  @ Fri, 06 Jan 2017 15:47:14: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:47:14: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:47:14: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:47:14: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:47:14: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:47:14: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:47:14: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:47:14: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:55:16: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:55:16: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:55:16: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:55:16: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:55:16: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:11:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:12:04: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 16:12:07: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 16:12:09: Done! 
INFO  @ Fri, 06 Jan 2017 16:12:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 16:12:16: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 16:12:16: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 16:12:24:  1000000 
INFO  @ Fri, 06 Jan 2017 16:12:31:  2000000 
INFO  @ Fri, 06 Jan 2017 16:12:38:  3000000 
INFO  @ Fri, 06 Jan 2017 16:12:45:  4000000 
INFO  @ Fri, 06 Jan 2017 16:12:52:  5000000 
INFO  @ Fri, 06 Jan 2017 16:13:00:  6000000 
INFO  @ Fri, 06 Jan 2017 16:13:08:  7000000 
INFO  @ Fri, 06 Jan 2017 16:13:11: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 16:13:19:  1000000 
INFO  @ Fri, 06 Jan 2017 16:13:26:  2000000 
INFO  @ Fri, 06 Jan 2017 16:13:33:  3000000 
INFO  @ Fri, 06 Jan 2017 16:13:40:  4000000 
INFO  @ Fri, 06 Jan 2017 16:13:47:  5000000 
INFO  @ Fri, 06 Jan 2017 16:13:54:  6000000 
INFO  @ Fri, 06 Jan 2017 16:14:01:  7000000 
INFO  @ Fri, 06 Jan 2017 16:14:08:  8000000 
INFO  @ Fri, 06 Jan 2017 16:14:15:  9000000 
INFO  @ Fri, 06 Jan 2017 16:14:22:  10000000 
INFO  @ Fri, 06 Jan 2017 16:14:30:  11000000 
INFO  @ Fri, 06 Jan 2017 16:14:37:  12000000 
INFO  @ Fri, 06 Jan 2017 16:14:45:  13000000 
INFO  @ Fri, 06 Jan 2017 16:14:52:  14000000 
INFO  @ Fri, 06 Jan 2017 16:14:58:  15000000 
INFO  @ Fri, 06 Jan 2017 16:15:05:  16000000 
INFO  @ Fri, 06 Jan 2017 16:15:12:  17000000 
INFO  @ Fri, 06 Jan 2017 16:15:19:  18000000 
INFO  @ Fri, 06 Jan 2017 16:15:26:  19000000 
INFO  @ Fri, 06 Jan 2017 16:15:33:  20000000 
INFO  @ Fri, 06 Jan 2017 16:15:40:  21000000 
INFO  @ Fri, 06 Jan 2017 16:15:47:  22000000 
INFO  @ Fri, 06 Jan 2017 16:15:54:  23000000 
INFO  @ Fri, 06 Jan 2017 16:16:02:  24000000 
INFO  @ Fri, 06 Jan 2017 16:16:09:  25000000 
INFO  @ Fri, 06 Jan 2017 16:16:17:  26000000 
INFO  @ Fri, 06 Jan 2017 16:16:24:  27000000 
INFO  @ Fri, 06 Jan 2017 16:16:31:  28000000 
INFO  @ Fri, 06 Jan 2017 16:16:38:  29000000 
INFO  @ Fri, 06 Jan 2017 16:16:45:  30000000 
INFO  @ Fri, 06 Jan 2017 16:16:52:  31000000 
INFO  @ Fri, 06 Jan 2017 16:16:59:  32000000 
INFO  @ Fri, 06 Jan 2017 16:17:07:  33000000 
INFO  @ Fri, 06 Jan 2017 16:17:14:  34000000 
INFO  @ Fri, 06 Jan 2017 16:17:21:  35000000 
INFO  @ Fri, 06 Jan 2017 16:17:27:  36000000 
INFO  @ Fri, 06 Jan 2017 16:17:35:  37000000 
INFO  @ Fri, 06 Jan 2017 16:17:42:  38000000 
INFO  @ Fri, 06 Jan 2017 16:17:49:  39000000 
INFO  @ Fri, 06 Jan 2017 16:17:57:  40000000 
INFO  @ Fri, 06 Jan 2017 16:18:04:  41000000 
INFO  @ Fri, 06 Jan 2017 16:18:11:  42000000 
INFO  @ Fri, 06 Jan 2017 16:18:18:  43000000 
INFO  @ Fri, 06 Jan 2017 16:18:25:  44000000 
INFO  @ Fri, 06 Jan 2017 16:18:33:  45000000 
INFO  @ Fri, 06 Jan 2017 16:18:40:  46000000 
INFO  @ Fri, 06 Jan 2017 16:18:47:  47000000 
INFO  @ Fri, 06 Jan 2017 16:18:54:  48000000 
INFO  @ Fri, 06 Jan 2017 16:19:01:  49000000 
INFO  @ Fri, 06 Jan 2017 16:19:09:  50000000 
INFO  @ Fri, 06 Jan 2017 16:19:13: #1 tag size is determined as 69 bps 
INFO  @ Fri, 06 Jan 2017 16:19:13: #1 tag size = 69 
INFO  @ Fri, 06 Jan 2017 16:19:13: #1  total tags in treatment: 7339739 
INFO  @ Fri, 06 Jan 2017 16:19:13: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 16:19:13: #1 finished! 
INFO  @ Fri, 06 Jan 2017 16:19:13: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 16:19:13: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 16:19:13: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 16:19:13: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 16:19:13: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 16:19:13: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:27:11: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:36:21: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:36:55: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:37:19: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:37:44: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24403

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

Start	2017-01-07 19:52:42
End	2017-01-07 19:53:52
Elapsed	00:01:10
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_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--------------------
43848 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000219.1	42646	42826	.	0	.	24.8190531804466	-1	3.7610144953249	90

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000219.1	42646	42826	.	0	.	24.8190531804466	-1	3.7610144953249	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2564	2744	.	0	.	31.5554888252011	-1	3.59194600653173	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196487.1	2564	2744	.	0	.	31.5554888252011	-1	3.59194600653173	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000208.1	74510	74690	.	0	.	6.39571757477632	-1	3.17089991460148	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000208.1	74510	74690	.	0	.	6.39571757477632	-1	3.17089991460148	90

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24404

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

Start	2017-01-07 19:53:54
End	2017-01-07 19:55:06
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370899_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370899_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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--------------------
43955 (process ID) old priority 0, new priority 10
Waiting for 23 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.30 1.25 0.78 0.37]
Number of reported peaks - 16657/16657 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 2769/16657 (16.6%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24405

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

Start	2017-01-07 19:55:07
End	2017-01-07 19:56:22
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/qc/ZNF264_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/ZNF264/out/qc/ZNF264_IDR_final.qc

# SYS command. line 224

 echo -e "0\t40	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/qc/ZNF264_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--------------------
44105 (process ID) old priority 0, new priority 10
Waiting for 59 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	52308

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

Start	2017-01-07 19:56:23
End	2017-01-07 19:57:31
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_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/ZNF264/out/peak/spp/rep1/SRR1370899_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--------------------
52312 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	42707	42784	.	0	.	49.4743803912797	-1	3.60863298949003	29

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/rep1/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	42707	42784	.	0	.	49.4743803912797	-1	3.60863298949003	29

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	56440

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

Start	2017-01-07 19:57:32
End	2017-01-07 19:57:41
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/spp/overlap/SRR1370899_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/ZNF264/out/peak/spp/overlap/SRR1370899_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
56444 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	57063

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

Start	2017-01-07 19:57:42
End	2017-01-07 19:57:50
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_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/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/peak/idr/pseudo_reps/rep1/ZNF264_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
57067 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	651

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

Start	2017-01-07 19:57:51
End	2017-01-07 19:57:59
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/ZNF264/out/report/ZNF264_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/report/ZNF264_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/report/ZNF264_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
658 (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, ZNF264, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF264/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF264/out/align/rep1/SRR1370899_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/ZNF264
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/ZNF264
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	46913.ZNF264.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