Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_144229_671
Start time	2017-01-06 14:42:29
Run time	2 days 00:41:17.030
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF467, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF467/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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_144229_671/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_144229_671/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_144229_671/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_144229_671/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_144229_671/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_144229_671/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_144229_671/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_144229_671/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_144229_671/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_144229_671/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_144229_671/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_144229_671/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_144229_671/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	24294

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

Start	2017-01-06 14:42:38
End	2017-01-08 15:12:22
Elapsed	2 days 00:29:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_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--------------------
38887 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_1.nodup.tagAlign.gz 
opened /tmp/24294.1.amd.q/RtmpU40inM/SRR1370886_1.nodup.tagAlign991c4674367f
done. read 18384762 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24294.1.amd.q/RtmpU40inM/input15MReadsNSCLess1.05.50MSubsample.tagAlign991c870052a
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.2015378 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.309554628167486 
Top 3 estimates for fragment length 145 
Window half size 300 
Phantom peak location 55 
Phantom peak Correlation 0.2657458 
Normalized Strand cross-correlation coefficient (NSC) 1.535963 
Relative Strand cross-correlation Coefficient (RSC) 1.682294 
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= 3.319483  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.3012517  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000041 
Detected 578993 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/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196484.1	173456	173756	.	0	.	46.2925214529174	-1	4.60705807900684	150

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196484.1	173456	173756	.	0	.	46.2925214529174	-1	4.60705807900684	150

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24295

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

Start	2017-01-06 14:42:39
End	2017-01-06 18:05:21
Elapsed	03:22:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/signal/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/signal/macs2/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1 -o "SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/signal/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1 -o "SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/signal/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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--------------------
38878 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:43:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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 14:43:00: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:43:00: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:43:08:  1000000 
INFO  @ Fri, 06 Jan 2017 14:43:15:  2000000 
INFO  @ Fri, 06 Jan 2017 14:43:23:  3000000 
INFO  @ Fri, 06 Jan 2017 14:43:30:  4000000 
INFO  @ Fri, 06 Jan 2017 14:43:38:  5000000 
INFO  @ Fri, 06 Jan 2017 14:43:46:  6000000 
INFO  @ Fri, 06 Jan 2017 14:43:54:  7000000 
INFO  @ Fri, 06 Jan 2017 14:44:01:  8000000 
INFO  @ Fri, 06 Jan 2017 14:44:09:  9000000 
INFO  @ Fri, 06 Jan 2017 14:44:16:  10000000 
INFO  @ Fri, 06 Jan 2017 14:44:24:  11000000 
INFO  @ Fri, 06 Jan 2017 14:44:31:  12000000 
INFO  @ Fri, 06 Jan 2017 14:44:39:  13000000 
INFO  @ Fri, 06 Jan 2017 14:44:47:  14000000 
INFO  @ Fri, 06 Jan 2017 14:44:55:  15000000 
INFO  @ Fri, 06 Jan 2017 14:45:02:  16000000 
INFO  @ Fri, 06 Jan 2017 14:45:09:  17000000 
INFO  @ Fri, 06 Jan 2017 14:45:16:  18000000 
INFO  @ Fri, 06 Jan 2017 14:45:20: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:45:27:  1000000 
INFO  @ Fri, 06 Jan 2017 14:45:36:  2000000 
INFO  @ Fri, 06 Jan 2017 14:45:44:  3000000 
INFO  @ Fri, 06 Jan 2017 14:45:51:  4000000 
INFO  @ Fri, 06 Jan 2017 14:45:59:  5000000 
INFO  @ Fri, 06 Jan 2017 14:46:07:  6000000 
INFO  @ Fri, 06 Jan 2017 14:46:14:  7000000 
INFO  @ Fri, 06 Jan 2017 14:46:23:  8000000 
INFO  @ Fri, 06 Jan 2017 14:46:31:  9000000 
INFO  @ Fri, 06 Jan 2017 14:46:38:  10000000 
INFO  @ Fri, 06 Jan 2017 14:46:46:  11000000 
INFO  @ Fri, 06 Jan 2017 14:46:54:  12000000 
INFO  @ Fri, 06 Jan 2017 14:47:02:  13000000 
INFO  @ Fri, 06 Jan 2017 14:47:09:  14000000 
INFO  @ Fri, 06 Jan 2017 14:47:18:  15000000 
INFO  @ Fri, 06 Jan 2017 14:47:26:  16000000 
INFO  @ Fri, 06 Jan 2017 14:47:34:  17000000 
INFO  @ Fri, 06 Jan 2017 14:47:42:  18000000 
INFO  @ Fri, 06 Jan 2017 14:47:50:  19000000 
INFO  @ Fri, 06 Jan 2017 14:47:58:  20000000 
INFO  @ Fri, 06 Jan 2017 14:48:07:  21000000 
INFO  @ Fri, 06 Jan 2017 14:48:15:  22000000 
INFO  @ Fri, 06 Jan 2017 14:48:23:  23000000 
INFO  @ Fri, 06 Jan 2017 14:48:32:  24000000 
INFO  @ Fri, 06 Jan 2017 14:48:39:  25000000 
INFO  @ Fri, 06 Jan 2017 14:48:47:  26000000 
INFO  @ Fri, 06 Jan 2017 14:48:55:  27000000 
INFO  @ Fri, 06 Jan 2017 14:49:04:  28000000 
INFO  @ Fri, 06 Jan 2017 14:49:12:  29000000 
INFO  @ Fri, 06 Jan 2017 14:49:20:  30000000 
INFO  @ Fri, 06 Jan 2017 14:49:28:  31000000 
INFO  @ Fri, 06 Jan 2017 14:49:36:  32000000 
INFO  @ Fri, 06 Jan 2017 14:49:44:  33000000 
INFO  @ Fri, 06 Jan 2017 14:49:52:  34000000 
INFO  @ Fri, 06 Jan 2017 14:50:00:  35000000 
INFO  @ Fri, 06 Jan 2017 14:50:08:  36000000 
INFO  @ Fri, 06 Jan 2017 14:50:16:  37000000 
INFO  @ Fri, 06 Jan 2017 14:50:23:  38000000 
INFO  @ Fri, 06 Jan 2017 14:50:31:  39000000 
INFO  @ Fri, 06 Jan 2017 14:50:38:  40000000 
INFO  @ Fri, 06 Jan 2017 14:50:46:  41000000 
INFO  @ Fri, 06 Jan 2017 14:50:53:  42000000 
INFO  @ Fri, 06 Jan 2017 14:51:01:  43000000 
INFO  @ Fri, 06 Jan 2017 14:51:09:  44000000 
INFO  @ Fri, 06 Jan 2017 14:51:17:  45000000 
INFO  @ Fri, 06 Jan 2017 14:51:26:  46000000 
INFO  @ Fri, 06 Jan 2017 14:51:34:  47000000 
INFO  @ Fri, 06 Jan 2017 14:51:42:  48000000 
INFO  @ Fri, 06 Jan 2017 14:51:49:  49000000 
INFO  @ Fri, 06 Jan 2017 14:51:57:  50000000 
INFO  @ Fri, 06 Jan 2017 14:52:01: #1 tag size is determined as 49 bps 
INFO  @ Fri, 06 Jan 2017 14:52:01: #1 tag size = 49 
INFO  @ Fri, 06 Jan 2017 14:52:01: #1  total tags in treatment: 18384762 
INFO  @ Fri, 06 Jan 2017 14:52:01: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:52:01: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:52:01: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:52:01: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:52:01: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:52:01: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:52:01: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:52:01: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:01:23: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:01:23: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:01:23: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:01:23: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:01:23: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:23:05: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:23:12: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:23:16: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:23:19: Done! 
INFO  @ Fri, 06 Jan 2017 15:23:27: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_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/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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 15:23:27: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:23:27: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:23:34:  1000000 
INFO  @ Fri, 06 Jan 2017 15:23:42:  2000000 
INFO  @ Fri, 06 Jan 2017 15:23:49:  3000000 
INFO  @ Fri, 06 Jan 2017 15:23:57:  4000000 
INFO  @ Fri, 06 Jan 2017 15:24:05:  5000000 
INFO  @ Fri, 06 Jan 2017 15:24:12:  6000000 
INFO  @ Fri, 06 Jan 2017 15:24:19:  7000000 
INFO  @ Fri, 06 Jan 2017 15:24:26:  8000000 
INFO  @ Fri, 06 Jan 2017 15:24:34:  9000000 
INFO  @ Fri, 06 Jan 2017 15:24:41:  10000000 
INFO  @ Fri, 06 Jan 2017 15:24:49:  11000000 
INFO  @ Fri, 06 Jan 2017 15:24:56:  12000000 
INFO  @ Fri, 06 Jan 2017 15:25:04:  13000000 
INFO  @ Fri, 06 Jan 2017 15:25:11:  14000000 
INFO  @ Fri, 06 Jan 2017 15:25:19:  15000000 
INFO  @ Fri, 06 Jan 2017 15:25:26:  16000000 
INFO  @ Fri, 06 Jan 2017 15:25:34:  17000000 
INFO  @ Fri, 06 Jan 2017 15:25:41:  18000000 
INFO  @ Fri, 06 Jan 2017 15:25:45: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:25:52:  1000000 
INFO  @ Fri, 06 Jan 2017 15:25:59:  2000000 
INFO  @ Fri, 06 Jan 2017 15:26:07:  3000000 
INFO  @ Fri, 06 Jan 2017 15:26:14:  4000000 
INFO  @ Fri, 06 Jan 2017 15:26:22:  5000000 
INFO  @ Fri, 06 Jan 2017 15:26:29:  6000000 
INFO  @ Fri, 06 Jan 2017 15:26:37:  7000000 
INFO  @ Fri, 06 Jan 2017 15:26:44:  8000000 
INFO  @ Fri, 06 Jan 2017 15:26:52:  9000000 
INFO  @ Fri, 06 Jan 2017 15:27:00:  10000000 
INFO  @ Fri, 06 Jan 2017 15:27:07:  11000000 
INFO  @ Fri, 06 Jan 2017 15:27:15:  12000000 
INFO  @ Fri, 06 Jan 2017 15:27:22:  13000000 
INFO  @ Fri, 06 Jan 2017 15:27:30:  14000000 
INFO  @ Fri, 06 Jan 2017 15:27:38:  15000000 
INFO  @ Fri, 06 Jan 2017 15:27:45:  16000000 
INFO  @ Fri, 06 Jan 2017 15:27:53:  17000000 
INFO  @ Fri, 06 Jan 2017 15:28:00:  18000000 
INFO  @ Fri, 06 Jan 2017 15:28:08:  19000000 
INFO  @ Fri, 06 Jan 2017 15:28:15:  20000000 
INFO  @ Fri, 06 Jan 2017 15:28:23:  21000000 
INFO  @ Fri, 06 Jan 2017 15:28:30:  22000000 
INFO  @ Fri, 06 Jan 2017 15:28:38:  23000000 
INFO  @ Fri, 06 Jan 2017 15:28:46:  24000000 
INFO  @ Fri, 06 Jan 2017 15:28:53:  25000000 
INFO  @ Fri, 06 Jan 2017 15:29:01:  26000000 
INFO  @ Fri, 06 Jan 2017 15:29:08:  27000000 
INFO  @ Fri, 06 Jan 2017 15:29:15:  28000000 
INFO  @ Fri, 06 Jan 2017 15:29:23:  29000000 
INFO  @ Fri, 06 Jan 2017 15:29:30:  30000000 
INFO  @ Fri, 06 Jan 2017 15:29:38:  31000000 
INFO  @ Fri, 06 Jan 2017 15:29:45:  32000000 
INFO  @ Fri, 06 Jan 2017 15:29:52:  33000000 
INFO  @ Fri, 06 Jan 2017 15:30:00:  34000000 
INFO  @ Fri, 06 Jan 2017 15:30:07:  35000000 
INFO  @ Fri, 06 Jan 2017 15:30:15:  36000000 
INFO  @ Fri, 06 Jan 2017 15:30:22:  37000000 
INFO  @ Fri, 06 Jan 2017 15:30:30:  38000000 
INFO  @ Fri, 06 Jan 2017 15:30:37:  39000000 
INFO  @ Fri, 06 Jan 2017 15:30:45:  40000000 
INFO  @ Fri, 06 Jan 2017 15:30:52:  41000000 
INFO  @ Fri, 06 Jan 2017 15:31:00:  42000000 
INFO  @ Fri, 06 Jan 2017 15:31:07:  43000000 
INFO  @ Fri, 06 Jan 2017 15:31:15:  44000000 
INFO  @ Fri, 06 Jan 2017 15:31:22:  45000000 
INFO  @ Fri, 06 Jan 2017 15:31:29:  46000000 
INFO  @ Fri, 06 Jan 2017 15:31:37:  47000000 
INFO  @ Fri, 06 Jan 2017 15:31:44:  48000000 
INFO  @ Fri, 06 Jan 2017 15:31:51:  49000000 
INFO  @ Fri, 06 Jan 2017 15:31:59:  50000000 
INFO  @ Fri, 06 Jan 2017 15:32:02: #1 tag size is determined as 49 bps 
INFO  @ Fri, 06 Jan 2017 15:32:02: #1 tag size = 49 
INFO  @ Fri, 06 Jan 2017 15:32:02: #1  total tags in treatment: 18384762 
INFO  @ Fri, 06 Jan 2017 15:32:02: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:32:02: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:32:02: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:32:02: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:32:02: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:32:02: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:32:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:32:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:40:34: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:48:32: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:48:49: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:48:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:49:08: Done! 
INFO  @ Fri, 06 Jan 2017 15:49:34: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:52:23: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:00:49: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:03:55: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:27:53: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:38:35: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:53:34: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:56:16: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 17:04:07: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 17:06:55: Values in your input bedGraph files will be multiplied by 18.384762 ... 
INFO  @ Fri, 06 Jan 2017 17:30:47: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:33:04: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:45:23: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/rep1/SRR1370886_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	24296

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

Start	2017-01-06 14:42:39
End	2017-01-08 10:20:35
Elapsed	1 day 19:37:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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--------------------
38881 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign.gz 
opened /tmp/24296.1.amd.q/RtmpsPxPmM/SRR1370886_1.nodup.pr1.tagAlign991b7231240c
done. read 9192381 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24296.1.amd.q/RtmpsPxPmM/input15MReadsNSCLess1.05.50MSubsample.tagAlign991b34e13866
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1188415 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.182494916862982 
Top 3 estimates for fragment length 145 
Window half size 300 
Phantom peak location 55 
Phantom peak Correlation 0.1565918 
Normalized Strand cross-correlation coefficient (NSC) 1.535616 
Relative Strand cross-correlation Coefficient (RSC) 1.686168 
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= 6.508057  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1536557  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000138 
Detected 279501 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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196484.1	173465	173765	.	0	.	29.3395437650447	-1	4.44083039840128	150

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196484.1	173465	173765	.	0	.	29.3395437650447	-1	4.44083039840128	150

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24297

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

Start	2017-01-06 14:42:41
End	2017-01-08 11:24:48
Elapsed	1 day 20:42:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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--------------------
38879 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.gz 
opened /tmp/24297.1.amd.q/RtmpRlclWS/SRR1370886_1.nodup.pr2.tagAlign992ddc3d4c7
done. read 9192381 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24297.1.amd.q/RtmpRlclWS/input15MReadsNSCLess1.05.50MSubsample.tagAlign992d59387849
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1182096 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.181445818216373 
Top 3 estimates for fragment length 145 
Window half size 305 
Phantom peak location 55 
Phantom peak Correlation 0.1559343 
Normalized Strand cross-correlation coefficient (NSC) 1.53495 
Relative Strand cross-correlation Coefficient (RSC) 1.676253 
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= 6.510609  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1535955  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000029 
Detected 279950 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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270830.1	16817	17121	.	0	.	22.2897406732018	-1	4.66634010803203	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270830.1	16817	17121	.	0	.	22.2897406732018	-1	4.66634010803203	152

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24298

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

Start	2017-01-06 14:42:42
End	2017-01-06 15:47:11
Elapsed	01:04:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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--------------------
38877 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:43:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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 14:43:01: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:43:01: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:43:10:  1000000 
INFO  @ Fri, 06 Jan 2017 14:43:18:  2000000 
INFO  @ Fri, 06 Jan 2017 14:43:26:  3000000 
INFO  @ Fri, 06 Jan 2017 14:43:34:  4000000 
INFO  @ Fri, 06 Jan 2017 14:43:42:  5000000 
INFO  @ Fri, 06 Jan 2017 14:43:50:  6000000 
INFO  @ Fri, 06 Jan 2017 14:43:58:  7000000 
INFO  @ Fri, 06 Jan 2017 14:44:06:  8000000 
INFO  @ Fri, 06 Jan 2017 14:44:14:  9000000 
INFO  @ Fri, 06 Jan 2017 14:44:17: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:44:24:  1000000 
INFO  @ Fri, 06 Jan 2017 14:44:32:  2000000 
INFO  @ Fri, 06 Jan 2017 14:44:40:  3000000 
INFO  @ Fri, 06 Jan 2017 14:44:48:  4000000 
INFO  @ Fri, 06 Jan 2017 14:44:56:  5000000 
INFO  @ Fri, 06 Jan 2017 14:45:05:  6000000 
INFO  @ Fri, 06 Jan 2017 14:45:13:  7000000 
INFO  @ Fri, 06 Jan 2017 14:45:22:  8000000 
INFO  @ Fri, 06 Jan 2017 14:45:30:  9000000 
INFO  @ Fri, 06 Jan 2017 14:45:38:  10000000 
INFO  @ Fri, 06 Jan 2017 14:45:46:  11000000 
INFO  @ Fri, 06 Jan 2017 14:45:54:  12000000 
INFO  @ Fri, 06 Jan 2017 14:46:02:  13000000 
INFO  @ Fri, 06 Jan 2017 14:46:10:  14000000 
INFO  @ Fri, 06 Jan 2017 14:46:18:  15000000 
INFO  @ Fri, 06 Jan 2017 14:46:27:  16000000 
INFO  @ Fri, 06 Jan 2017 14:46:35:  17000000 
INFO  @ Fri, 06 Jan 2017 14:46:44:  18000000 
INFO  @ Fri, 06 Jan 2017 14:46:52:  19000000 
INFO  @ Fri, 06 Jan 2017 14:47:00:  20000000 
INFO  @ Fri, 06 Jan 2017 14:47:08:  21000000 
INFO  @ Fri, 06 Jan 2017 14:47:16:  22000000 
INFO  @ Fri, 06 Jan 2017 14:47:24:  23000000 
INFO  @ Fri, 06 Jan 2017 14:47:33:  24000000 
INFO  @ Fri, 06 Jan 2017 14:47:41:  25000000 
INFO  @ Fri, 06 Jan 2017 14:47:48:  26000000 
INFO  @ Fri, 06 Jan 2017 14:47:57:  27000000 
INFO  @ Fri, 06 Jan 2017 14:48:04:  28000000 
INFO  @ Fri, 06 Jan 2017 14:48:12:  29000000 
INFO  @ Fri, 06 Jan 2017 14:48:21:  30000000 
INFO  @ Fri, 06 Jan 2017 14:48:29:  31000000 
INFO  @ Fri, 06 Jan 2017 14:48:36:  32000000 
INFO  @ Fri, 06 Jan 2017 14:48:43:  33000000 
INFO  @ Fri, 06 Jan 2017 14:48:51:  34000000 
INFO  @ Fri, 06 Jan 2017 14:48:58:  35000000 
INFO  @ Fri, 06 Jan 2017 14:49:05:  36000000 
INFO  @ Fri, 06 Jan 2017 14:49:13:  37000000 
INFO  @ Fri, 06 Jan 2017 14:49:20:  38000000 
INFO  @ Fri, 06 Jan 2017 14:49:29:  39000000 
INFO  @ Fri, 06 Jan 2017 14:49:36:  40000000 
INFO  @ Fri, 06 Jan 2017 14:49:43:  41000000 
INFO  @ Fri, 06 Jan 2017 14:49:51:  42000000 
INFO  @ Fri, 06 Jan 2017 14:49:58:  43000000 
INFO  @ Fri, 06 Jan 2017 14:50:06:  44000000 
INFO  @ Fri, 06 Jan 2017 14:50:15:  45000000 
INFO  @ Fri, 06 Jan 2017 14:50:24:  46000000 
INFO  @ Fri, 06 Jan 2017 14:50:33:  47000000 
INFO  @ Fri, 06 Jan 2017 14:50:42:  48000000 
INFO  @ Fri, 06 Jan 2017 14:50:50:  49000000 
INFO  @ Fri, 06 Jan 2017 14:50:59:  50000000 
INFO  @ Fri, 06 Jan 2017 14:51:03: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 14:51:03: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 14:51:03: #1  total tags in treatment: 9192381 
INFO  @ Fri, 06 Jan 2017 14:51:03: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:51:03: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:51:03: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:51:03: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:51:03: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:51:03: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:51:03: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:51:03: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:59:45: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:59:45: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:59:45: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:59:45: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:59:45: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:18:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:18:14: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:18:18: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:18:21: Done! 
INFO  @ Fri, 06 Jan 2017 15:18:30: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr1/SRR1370886_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 15:18:30: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:18:30: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:18:39:  1000000 
INFO  @ Fri, 06 Jan 2017 15:18:47:  2000000 
INFO  @ Fri, 06 Jan 2017 15:18:55:  3000000 
INFO  @ Fri, 06 Jan 2017 15:19:03:  4000000 
INFO  @ Fri, 06 Jan 2017 15:19:11:  5000000 
INFO  @ Fri, 06 Jan 2017 15:19:20:  6000000 
INFO  @ Fri, 06 Jan 2017 15:19:28:  7000000 
INFO  @ Fri, 06 Jan 2017 15:19:36:  8000000 
INFO  @ Fri, 06 Jan 2017 15:19:44:  9000000 
INFO  @ Fri, 06 Jan 2017 15:19:47: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:19:55:  1000000 
INFO  @ Fri, 06 Jan 2017 15:20:03:  2000000 
INFO  @ Fri, 06 Jan 2017 15:20:11:  3000000 
INFO  @ Fri, 06 Jan 2017 15:20:19:  4000000 
INFO  @ Fri, 06 Jan 2017 15:20:27:  5000000 
INFO  @ Fri, 06 Jan 2017 15:20:36:  6000000 
INFO  @ Fri, 06 Jan 2017 15:20:44:  7000000 
INFO  @ Fri, 06 Jan 2017 15:20:53:  8000000 
INFO  @ Fri, 06 Jan 2017 15:21:00:  9000000 
INFO  @ Fri, 06 Jan 2017 15:21:09:  10000000 
INFO  @ Fri, 06 Jan 2017 15:21:17:  11000000 
INFO  @ Fri, 06 Jan 2017 15:21:26:  12000000 
INFO  @ Fri, 06 Jan 2017 15:21:35:  13000000 
INFO  @ Fri, 06 Jan 2017 15:21:43:  14000000 
INFO  @ Fri, 06 Jan 2017 15:21:52:  15000000 
INFO  @ Fri, 06 Jan 2017 15:22:00:  16000000 
INFO  @ Fri, 06 Jan 2017 15:22:09:  17000000 
INFO  @ Fri, 06 Jan 2017 15:22:18:  18000000 
INFO  @ Fri, 06 Jan 2017 15:22:27:  19000000 
INFO  @ Fri, 06 Jan 2017 15:22:35:  20000000 
INFO  @ Fri, 06 Jan 2017 15:22:43:  21000000 
INFO  @ Fri, 06 Jan 2017 15:22:52:  22000000 
INFO  @ Fri, 06 Jan 2017 15:23:00:  23000000 
INFO  @ Fri, 06 Jan 2017 15:23:08:  24000000 
INFO  @ Fri, 06 Jan 2017 15:23:16:  25000000 
INFO  @ Fri, 06 Jan 2017 15:23:25:  26000000 
INFO  @ Fri, 06 Jan 2017 15:23:33:  27000000 
INFO  @ Fri, 06 Jan 2017 15:23:41:  28000000 
INFO  @ Fri, 06 Jan 2017 15:23:49:  29000000 
INFO  @ Fri, 06 Jan 2017 15:23:57:  30000000 
INFO  @ Fri, 06 Jan 2017 15:24:05:  31000000 
INFO  @ Fri, 06 Jan 2017 15:24:13:  32000000 
INFO  @ Fri, 06 Jan 2017 15:24:21:  33000000 
INFO  @ Fri, 06 Jan 2017 15:24:29:  34000000 
INFO  @ Fri, 06 Jan 2017 15:24:37:  35000000 
INFO  @ Fri, 06 Jan 2017 15:24:46:  36000000 
INFO  @ Fri, 06 Jan 2017 15:24:54:  37000000 
INFO  @ Fri, 06 Jan 2017 15:25:02:  38000000 
INFO  @ Fri, 06 Jan 2017 15:25:10:  39000000 
INFO  @ Fri, 06 Jan 2017 15:25:18:  40000000 
INFO  @ Fri, 06 Jan 2017 15:25:26:  41000000 
INFO  @ Fri, 06 Jan 2017 15:25:34:  42000000 
INFO  @ Fri, 06 Jan 2017 15:25:42:  43000000 
INFO  @ Fri, 06 Jan 2017 15:25:51:  44000000 
INFO  @ Fri, 06 Jan 2017 15:25:59:  45000000 
INFO  @ Fri, 06 Jan 2017 15:26:07:  46000000 
INFO  @ Fri, 06 Jan 2017 15:26:15:  47000000 
INFO  @ Fri, 06 Jan 2017 15:26:23:  48000000 
INFO  @ Fri, 06 Jan 2017 15:26:31:  49000000 
INFO  @ Fri, 06 Jan 2017 15:26:40:  50000000 
INFO  @ Fri, 06 Jan 2017 15:26:44: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:26:44: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:26:44: #1  total tags in treatment: 9192381 
INFO  @ Fri, 06 Jan 2017 15:26:44: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:26:44: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:26:44: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:26:44: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:26:44: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:26:44: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:26:44: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:26:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:36:11: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:45:36: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:46:04: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:46:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:46:38: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24338

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

Start	2017-01-06 15:47:14
End	2017-01-06 16:06:06
Elapsed	00:18:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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--------------------
10224 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:47:38: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 15:47:38: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:47:38: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:47:40:  1000000 
INFO  @ Fri, 06 Jan 2017 15:47:42:  2000000 
INFO  @ Fri, 06 Jan 2017 15:47:44:  3000000 
INFO  @ Fri, 06 Jan 2017 15:47:45:  4000000 
INFO  @ Fri, 06 Jan 2017 15:47:47:  5000000 
INFO  @ Fri, 06 Jan 2017 15:47:49:  6000000 
INFO  @ Fri, 06 Jan 2017 15:47:51:  7000000 
INFO  @ Fri, 06 Jan 2017 15:47:53:  8000000 
INFO  @ Fri, 06 Jan 2017 15:47:55:  9000000 
INFO  @ Fri, 06 Jan 2017 15:47:56: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:47:58:  1000000 
INFO  @ Fri, 06 Jan 2017 15:47:59:  2000000 
INFO  @ Fri, 06 Jan 2017 15:48:01:  3000000 
INFO  @ Fri, 06 Jan 2017 15:48:02:  4000000 
INFO  @ Fri, 06 Jan 2017 15:48:05:  5000000 
INFO  @ Fri, 06 Jan 2017 15:48:06:  6000000 
INFO  @ Fri, 06 Jan 2017 15:48:08:  7000000 
INFO  @ Fri, 06 Jan 2017 15:48:10:  8000000 
INFO  @ Fri, 06 Jan 2017 15:48:12:  9000000 
INFO  @ Fri, 06 Jan 2017 15:48:14:  10000000 
INFO  @ Fri, 06 Jan 2017 15:48:16:  11000000 
INFO  @ Fri, 06 Jan 2017 15:48:18:  12000000 
INFO  @ Fri, 06 Jan 2017 15:48:20:  13000000 
INFO  @ Fri, 06 Jan 2017 15:48:21:  14000000 
INFO  @ Fri, 06 Jan 2017 15:48:23:  15000000 
INFO  @ Fri, 06 Jan 2017 15:48:25:  16000000 
INFO  @ Fri, 06 Jan 2017 15:48:27:  17000000 
INFO  @ Fri, 06 Jan 2017 15:48:29:  18000000 
INFO  @ Fri, 06 Jan 2017 15:48:31:  19000000 
INFO  @ Fri, 06 Jan 2017 15:48:32:  20000000 
INFO  @ Fri, 06 Jan 2017 15:48:34:  21000000 
INFO  @ Fri, 06 Jan 2017 15:48:35:  22000000 
INFO  @ Fri, 06 Jan 2017 15:48:37:  23000000 
INFO  @ Fri, 06 Jan 2017 15:48:39:  24000000 
INFO  @ Fri, 06 Jan 2017 15:48:41:  25000000 
INFO  @ Fri, 06 Jan 2017 15:48:42:  26000000 
INFO  @ Fri, 06 Jan 2017 15:48:44:  27000000 
INFO  @ Fri, 06 Jan 2017 15:48:46:  28000000 
INFO  @ Fri, 06 Jan 2017 15:48:48:  29000000 
INFO  @ Fri, 06 Jan 2017 15:48:50:  30000000 
INFO  @ Fri, 06 Jan 2017 15:48:52:  31000000 
INFO  @ Fri, 06 Jan 2017 15:48:53:  32000000 
INFO  @ Fri, 06 Jan 2017 15:48:55:  33000000 
INFO  @ Fri, 06 Jan 2017 15:48:57:  34000000 
INFO  @ Fri, 06 Jan 2017 15:48:58:  35000000 
INFO  @ Fri, 06 Jan 2017 15:49:00:  36000000 
INFO  @ Fri, 06 Jan 2017 15:49:02:  37000000 
INFO  @ Fri, 06 Jan 2017 15:49:04:  38000000 
INFO  @ Fri, 06 Jan 2017 15:49:05:  39000000 
INFO  @ Fri, 06 Jan 2017 15:49:07:  40000000 
INFO  @ Fri, 06 Jan 2017 15:49:09:  41000000 
INFO  @ Fri, 06 Jan 2017 15:49:11:  42000000 
INFO  @ Fri, 06 Jan 2017 15:49:12:  43000000 
INFO  @ Fri, 06 Jan 2017 15:49:14:  44000000 
INFO  @ Fri, 06 Jan 2017 15:49:16:  45000000 
INFO  @ Fri, 06 Jan 2017 15:49:17:  46000000 
INFO  @ Fri, 06 Jan 2017 15:49:19:  47000000 
INFO  @ Fri, 06 Jan 2017 15:49:20:  48000000 
INFO  @ Fri, 06 Jan 2017 15:49:22:  49000000 
INFO  @ Fri, 06 Jan 2017 15:49:24:  50000000 
INFO  @ Fri, 06 Jan 2017 15:49:25: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:49:25: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:49:25: #1  total tags in treatment: 9192381 
INFO  @ Fri, 06 Jan 2017 15:49:25: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:49:25: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:49:25: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:49:25: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:49:25: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:49:25: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:49:25: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:49:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:52:32: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:52:32: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:52:32: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:52:32: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:52:32: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:57:43: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:57:44: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:57:45: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:57:46: Done! 
INFO  @ Fri, 06 Jan 2017 15:57:50: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 15:57:50: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:57:50: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:57:52:  1000000 
INFO  @ Fri, 06 Jan 2017 15:57:54:  2000000 
INFO  @ Fri, 06 Jan 2017 15:57:56:  3000000 
INFO  @ Fri, 06 Jan 2017 15:57:58:  4000000 
INFO  @ Fri, 06 Jan 2017 15:58:00:  5000000 
INFO  @ Fri, 06 Jan 2017 15:58:02:  6000000 
INFO  @ Fri, 06 Jan 2017 15:58:04:  7000000 
INFO  @ Fri, 06 Jan 2017 15:58:06:  8000000 
INFO  @ Fri, 06 Jan 2017 15:58:08:  9000000 
INFO  @ Fri, 06 Jan 2017 15:58:09: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:58:11:  1000000 
INFO  @ Fri, 06 Jan 2017 15:58:13:  2000000 
INFO  @ Fri, 06 Jan 2017 15:58:15:  3000000 
INFO  @ Fri, 06 Jan 2017 15:58:17:  4000000 
INFO  @ Fri, 06 Jan 2017 15:58:19:  5000000 
INFO  @ Fri, 06 Jan 2017 15:58:20:  6000000 
INFO  @ Fri, 06 Jan 2017 15:58:22:  7000000 
INFO  @ Fri, 06 Jan 2017 15:58:24:  8000000 
INFO  @ Fri, 06 Jan 2017 15:58:26:  9000000 
INFO  @ Fri, 06 Jan 2017 15:58:28:  10000000 
INFO  @ Fri, 06 Jan 2017 15:58:30:  11000000 
INFO  @ Fri, 06 Jan 2017 15:58:32:  12000000 
INFO  @ Fri, 06 Jan 2017 15:58:33:  13000000 
INFO  @ Fri, 06 Jan 2017 15:58:35:  14000000 
INFO  @ Fri, 06 Jan 2017 15:58:37:  15000000 
INFO  @ Fri, 06 Jan 2017 15:58:38:  16000000 
INFO  @ Fri, 06 Jan 2017 15:58:40:  17000000 
INFO  @ Fri, 06 Jan 2017 15:58:42:  18000000 
INFO  @ Fri, 06 Jan 2017 15:58:44:  19000000 
INFO  @ Fri, 06 Jan 2017 15:58:46:  20000000 
INFO  @ Fri, 06 Jan 2017 15:58:47:  21000000 
INFO  @ Fri, 06 Jan 2017 15:58:49:  22000000 
INFO  @ Fri, 06 Jan 2017 15:58:51:  23000000 
INFO  @ Fri, 06 Jan 2017 15:58:53:  24000000 
INFO  @ Fri, 06 Jan 2017 15:58:55:  25000000 
INFO  @ Fri, 06 Jan 2017 15:58:57:  26000000 
INFO  @ Fri, 06 Jan 2017 15:58:58:  27000000 
INFO  @ Fri, 06 Jan 2017 15:59:00:  28000000 
INFO  @ Fri, 06 Jan 2017 15:59:02:  29000000 
INFO  @ Fri, 06 Jan 2017 15:59:04:  30000000 
INFO  @ Fri, 06 Jan 2017 15:59:05:  31000000 
INFO  @ Fri, 06 Jan 2017 15:59:07:  32000000 
INFO  @ Fri, 06 Jan 2017 15:59:09:  33000000 
INFO  @ Fri, 06 Jan 2017 15:59:10:  34000000 
INFO  @ Fri, 06 Jan 2017 15:59:12:  35000000 
INFO  @ Fri, 06 Jan 2017 15:59:14:  36000000 
INFO  @ Fri, 06 Jan 2017 15:59:16:  37000000 
INFO  @ Fri, 06 Jan 2017 15:59:18:  38000000 
INFO  @ Fri, 06 Jan 2017 15:59:20:  39000000 
INFO  @ Fri, 06 Jan 2017 15:59:22:  40000000 
INFO  @ Fri, 06 Jan 2017 15:59:24:  41000000 
INFO  @ Fri, 06 Jan 2017 15:59:25:  42000000 
INFO  @ Fri, 06 Jan 2017 15:59:27:  43000000 
INFO  @ Fri, 06 Jan 2017 15:59:29:  44000000 
INFO  @ Fri, 06 Jan 2017 15:59:30:  45000000 
INFO  @ Fri, 06 Jan 2017 15:59:32:  46000000 
INFO  @ Fri, 06 Jan 2017 15:59:34:  47000000 
INFO  @ Fri, 06 Jan 2017 15:59:36:  48000000 
INFO  @ Fri, 06 Jan 2017 15:59:37:  49000000 
INFO  @ Fri, 06 Jan 2017 15:59:39:  50000000 
INFO  @ Fri, 06 Jan 2017 15:59:41: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:59:41: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:59:41: #1  total tags in treatment: 9192381 
INFO  @ Fri, 06 Jan 2017 15:59:41: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:59:41: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:59:41: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:59:41: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:59:41: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:59:41: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:59:41: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:59:41: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:02:47: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:05:38: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:05:43: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:05:48: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:05:52: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24517

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

Start	2017-01-08 15:12:23
End	2017-01-08 15:13:42
Elapsed	00:01:19
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_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--------------------
51248 (process ID) old priority 0, new priority 10
Waiting for 49 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	173465	173765	.	0	.	29.3395437650447	-1	4.44083039840128	150

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KN196484.1	173465	173765	.	0	.	29.3395437650447	-1	4.44083039840128	150

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1	16817	17121	.	0	.	22.2897406732018	-1	4.66634010803203	152

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270830.1	16817	17121	.	0	.	22.2897406732018	-1	4.66634010803203	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	137464	137764	.	0	.	10.7826308108124	-1	3.9234063736463	150

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	137464	137764	.	0	.	10.7826308108124	-1	3.9234063736463	150

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24521

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

Start	2017-01-08 15:13:43
End	2017-01-08 15:20:53
Elapsed	00:07:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370886_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370886_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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--------------------
51499 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.56 1.27 0.87 0.48]
Number of reported peaks - 118104/118104 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 35443/118104 (30.0%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24525

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

Start	2017-01-08 15:20:55
End	2017-01-08 15:22:07
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/qc/ZNF467_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/ZNF467/out/qc/ZNF467_IDR_final.qc

# SYS command. line 224

 echo -e "0\t864	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/qc/ZNF467_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--------------------
9224 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

Num	10
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21
Name	blacklist_filter peak 1
Thread	thread_Root
PID	42637

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

Start	2017-01-08 15:22:09
End	2017-01-08 15:23:17
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_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/ZNF467/out/peak/spp/rep1/SRR1370886_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--------------------
42641 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196484.1	173456	173756	.	0	.	46.2925214529174	-1	4.60705807900684	150

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/rep1/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196484.1	173456	173756	.	0	.	46.2925214529174	-1	4.60705807900684	150

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	46366

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

Start	2017-01-08 15:23:18
End	2017-01-08 15:23:27
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/spp/overlap/SRR1370886_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/ZNF467/out/peak/spp/overlap/SRR1370886_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
46370 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	46931

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

Start	2017-01-08 15:23:28
End	2017-01-08 15:23:36
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_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/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/peak/idr/pseudo_reps/rep1/ZNF467_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
46935 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	47491

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

Start	2017-01-08 15:23:37
End	2017-01-08 15:23:46
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/ZNF467/out/report/ZNF467_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/report/ZNF467_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/report/ZNF467_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
47495 (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, ZNF467, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF467/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF467/out/align/rep1/SRR1370886_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/ZNF467
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/ZNF467
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	16928.ZNF467.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