Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_143703_995
Start time	2017-01-06 14:37:04
Run time	2 days 03:40:12.166
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF322, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF322/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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_143703_995/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_143703_995/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_143703_995/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_143703_995/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_143703_995/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_143703_995/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_143703_995/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_143703_995/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_143703_995/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_143703_995/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_143703_995/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_143703_995/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_143703_995/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	24265

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

Start	2017-01-06 14:37:10
End	2017-01-08 18:10:09
Elapsed	2 days 03:32:58
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_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--------------------
35684 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_1.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/align/rep1/SRR1370894_1.nodup.tagAlign.gz 
opened /tmp/24265.1.amd.q/Rtmp6j0Pe4/SRR1370894_1.nodup.tagAlign8be02c91247
done. read 20891566 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24265.1.amd.q/Rtmp6j0Pe4/input15MReadsNSCLess1.05.50MSubsample.tagAlign8be047797838
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.2188786 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.269711923827603 
Top 3 estimates for fragment length 160 
Window half size 305 
Phantom peak location 55 
Phantom peak Correlation 0.245748 
Normalized Strand cross-correlation coefficient (NSC) 1.232245 
Relative Strand cross-correlation Coefficient (RSC) 1.891868 
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= 2.528231  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.3955335  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000038 
Detected 729799 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/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	99419	99581	.	0	.	76.7788412093407	-1	4.46898205896257	73

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	99419	99581	.	0	.	76.7788412093407	-1	4.46898205896257	73

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24266

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

Start	2017-01-06 14:37:11
End	2017-01-06 18:06:41
Elapsed	03:29:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/signal/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/signal/macs2/rep1/SRR1370894_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/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1 -o "SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/signal/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1 -o "SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/signal/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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--------------------
35683 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:37:27: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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 14:37:27: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:37:27: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:37:34:  1000000 
INFO  @ Fri, 06 Jan 2017 14:37:40:  2000000 
INFO  @ Fri, 06 Jan 2017 14:37:46:  3000000 
INFO  @ Fri, 06 Jan 2017 14:37:53:  4000000 
INFO  @ Fri, 06 Jan 2017 14:37:59:  5000000 
INFO  @ Fri, 06 Jan 2017 14:38:05:  6000000 
INFO  @ Fri, 06 Jan 2017 14:38:11:  7000000 
INFO  @ Fri, 06 Jan 2017 14:38:18:  8000000 
INFO  @ Fri, 06 Jan 2017 14:38:25:  9000000 
INFO  @ Fri, 06 Jan 2017 14:38:31:  10000000 
INFO  @ Fri, 06 Jan 2017 14:38:37:  11000000 
INFO  @ Fri, 06 Jan 2017 14:38:43:  12000000 
INFO  @ Fri, 06 Jan 2017 14:38:50:  13000000 
INFO  @ Fri, 06 Jan 2017 14:38:56:  14000000 
INFO  @ Fri, 06 Jan 2017 14:39:03:  15000000 
INFO  @ Fri, 06 Jan 2017 14:39:10:  16000000 
INFO  @ Fri, 06 Jan 2017 14:39:18:  17000000 
INFO  @ Fri, 06 Jan 2017 14:39:26:  18000000 
INFO  @ Fri, 06 Jan 2017 14:39:33:  19000000 
INFO  @ Fri, 06 Jan 2017 14:39:41:  20000000 
INFO  @ Fri, 06 Jan 2017 14:39:48: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:39:55:  1000000 
INFO  @ Fri, 06 Jan 2017 14:40:03:  2000000 
INFO  @ Fri, 06 Jan 2017 14:40:10:  3000000 
INFO  @ Fri, 06 Jan 2017 14:40:18:  4000000 
INFO  @ Fri, 06 Jan 2017 14:40:24:  5000000 
INFO  @ Fri, 06 Jan 2017 14:40:31:  6000000 
INFO  @ Fri, 06 Jan 2017 14:40:38:  7000000 
INFO  @ Fri, 06 Jan 2017 14:40:45:  8000000 
INFO  @ Fri, 06 Jan 2017 14:40:52:  9000000 
INFO  @ Fri, 06 Jan 2017 14:40:58:  10000000 
INFO  @ Fri, 06 Jan 2017 14:41:05:  11000000 
INFO  @ Fri, 06 Jan 2017 14:41:12:  12000000 
INFO  @ Fri, 06 Jan 2017 14:41:19:  13000000 
INFO  @ Fri, 06 Jan 2017 14:41:26:  14000000 
INFO  @ Fri, 06 Jan 2017 14:41:34:  15000000 
INFO  @ Fri, 06 Jan 2017 14:41:41:  16000000 
INFO  @ Fri, 06 Jan 2017 14:41:49:  17000000 
INFO  @ Fri, 06 Jan 2017 14:41:57:  18000000 
INFO  @ Fri, 06 Jan 2017 14:42:04:  19000000 
INFO  @ Fri, 06 Jan 2017 14:42:12:  20000000 
INFO  @ Fri, 06 Jan 2017 14:42:19:  21000000 
INFO  @ Fri, 06 Jan 2017 14:42:27:  22000000 
INFO  @ Fri, 06 Jan 2017 14:42:35:  23000000 
INFO  @ Fri, 06 Jan 2017 14:42:43:  24000000 
INFO  @ Fri, 06 Jan 2017 14:42:51:  25000000 
INFO  @ Fri, 06 Jan 2017 14:42:58:  26000000 
INFO  @ Fri, 06 Jan 2017 14:43:06:  27000000 
INFO  @ Fri, 06 Jan 2017 14:43:13:  28000000 
INFO  @ Fri, 06 Jan 2017 14:43:21:  29000000 
INFO  @ Fri, 06 Jan 2017 14:43:29:  30000000 
INFO  @ Fri, 06 Jan 2017 14:43:37:  31000000 
INFO  @ Fri, 06 Jan 2017 14:43:45:  32000000 
INFO  @ Fri, 06 Jan 2017 14:43:53:  33000000 
INFO  @ Fri, 06 Jan 2017 14:44:00:  34000000 
INFO  @ Fri, 06 Jan 2017 14:44:08:  35000000 
INFO  @ Fri, 06 Jan 2017 14:44:16:  36000000 
INFO  @ Fri, 06 Jan 2017 14:44:24:  37000000 
INFO  @ Fri, 06 Jan 2017 14:44:31:  38000000 
INFO  @ Fri, 06 Jan 2017 14:44:39:  39000000 
INFO  @ Fri, 06 Jan 2017 14:44:47:  40000000 
INFO  @ Fri, 06 Jan 2017 14:44:55:  41000000 
INFO  @ Fri, 06 Jan 2017 14:45:02:  42000000 
INFO  @ Fri, 06 Jan 2017 14:45:10:  43000000 
INFO  @ Fri, 06 Jan 2017 14:45:18:  44000000 
INFO  @ Fri, 06 Jan 2017 14:45:25:  45000000 
INFO  @ Fri, 06 Jan 2017 14:45:33:  46000000 
INFO  @ Fri, 06 Jan 2017 14:45:40:  47000000 
INFO  @ Fri, 06 Jan 2017 14:45:48:  48000000 
INFO  @ Fri, 06 Jan 2017 14:45:55:  49000000 
INFO  @ Fri, 06 Jan 2017 14:46:03:  50000000 
INFO  @ Fri, 06 Jan 2017 14:46:07: #1 tag size is determined as 49 bps 
INFO  @ Fri, 06 Jan 2017 14:46:07: #1 tag size = 49 
INFO  @ Fri, 06 Jan 2017 14:46:07: #1  total tags in treatment: 20891566 
INFO  @ Fri, 06 Jan 2017 14:46:07: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:46:07: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:46:07: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:46:07: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:46:07: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:46:07: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:46:07: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:46:07: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:55:44: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:55:44: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:55:44: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:55:44: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:55:44: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:18:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:18:40: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:18:43: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:18:47: Done! 
INFO  @ Fri, 06 Jan 2017 15:18:54: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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 15:18:54: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:18:54: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:19:02:  1000000 
INFO  @ Fri, 06 Jan 2017 15:19:09:  2000000 
INFO  @ Fri, 06 Jan 2017 15:19:17:  3000000 
INFO  @ Fri, 06 Jan 2017 15:19:25:  4000000 
INFO  @ Fri, 06 Jan 2017 15:19:32:  5000000 
INFO  @ Fri, 06 Jan 2017 15:19:40:  6000000 
INFO  @ Fri, 06 Jan 2017 15:19:47:  7000000 
INFO  @ Fri, 06 Jan 2017 15:19:55:  8000000 
INFO  @ Fri, 06 Jan 2017 15:20:02:  9000000 
INFO  @ Fri, 06 Jan 2017 15:20:10:  10000000 
INFO  @ Fri, 06 Jan 2017 15:20:18:  11000000 
INFO  @ Fri, 06 Jan 2017 15:20:25:  12000000 
INFO  @ Fri, 06 Jan 2017 15:20:33:  13000000 
INFO  @ Fri, 06 Jan 2017 15:20:42:  14000000 
INFO  @ Fri, 06 Jan 2017 15:20:50:  15000000 
INFO  @ Fri, 06 Jan 2017 15:20:58:  16000000 
INFO  @ Fri, 06 Jan 2017 15:21:05:  17000000 
INFO  @ Fri, 06 Jan 2017 15:21:13:  18000000 
INFO  @ Fri, 06 Jan 2017 15:21:20:  19000000 
INFO  @ Fri, 06 Jan 2017 15:21:27:  20000000 
INFO  @ Fri, 06 Jan 2017 15:21:35: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:21:43:  1000000 
INFO  @ Fri, 06 Jan 2017 15:21:50:  2000000 
INFO  @ Fri, 06 Jan 2017 15:21:57:  3000000 
INFO  @ Fri, 06 Jan 2017 15:22:05:  4000000 
INFO  @ Fri, 06 Jan 2017 15:22:13:  5000000 
INFO  @ Fri, 06 Jan 2017 15:22:20:  6000000 
INFO  @ Fri, 06 Jan 2017 15:22:27:  7000000 
INFO  @ Fri, 06 Jan 2017 15:22:35:  8000000 
INFO  @ Fri, 06 Jan 2017 15:22:43:  9000000 
INFO  @ Fri, 06 Jan 2017 15:22:50:  10000000 
INFO  @ Fri, 06 Jan 2017 15:22:58:  11000000 
INFO  @ Fri, 06 Jan 2017 15:23:06:  12000000 
INFO  @ Fri, 06 Jan 2017 15:23:13:  13000000 
INFO  @ Fri, 06 Jan 2017 15:23:21:  14000000 
INFO  @ Fri, 06 Jan 2017 15:23:28:  15000000 
INFO  @ Fri, 06 Jan 2017 15:23:36:  16000000 
INFO  @ Fri, 06 Jan 2017 15:23:44:  17000000 
INFO  @ Fri, 06 Jan 2017 15:23:52:  18000000 
INFO  @ Fri, 06 Jan 2017 15:23:59:  19000000 
INFO  @ Fri, 06 Jan 2017 15:24:07:  20000000 
INFO  @ Fri, 06 Jan 2017 15:24:15:  21000000 
INFO  @ Fri, 06 Jan 2017 15:24:23:  22000000 
INFO  @ Fri, 06 Jan 2017 15:24:31:  23000000 
INFO  @ Fri, 06 Jan 2017 15:24:38:  24000000 
INFO  @ Fri, 06 Jan 2017 15:24:46:  25000000 
INFO  @ Fri, 06 Jan 2017 15:24:53:  26000000 
INFO  @ Fri, 06 Jan 2017 15:25:01:  27000000 
INFO  @ Fri, 06 Jan 2017 15:25:08:  28000000 
INFO  @ Fri, 06 Jan 2017 15:25:16:  29000000 
INFO  @ Fri, 06 Jan 2017 15:25:24:  30000000 
INFO  @ Fri, 06 Jan 2017 15:25:31:  31000000 
INFO  @ Fri, 06 Jan 2017 15:25:39:  32000000 
INFO  @ Fri, 06 Jan 2017 15:25:47:  33000000 
INFO  @ Fri, 06 Jan 2017 15:25:54:  34000000 
INFO  @ Fri, 06 Jan 2017 15:26:02:  35000000 
INFO  @ Fri, 06 Jan 2017 15:26:09:  36000000 
INFO  @ Fri, 06 Jan 2017 15:26:17:  37000000 
INFO  @ Fri, 06 Jan 2017 15:26:25:  38000000 
INFO  @ Fri, 06 Jan 2017 15:26:33:  39000000 
INFO  @ Fri, 06 Jan 2017 15:26:41:  40000000 
INFO  @ Fri, 06 Jan 2017 15:26:48:  41000000 
INFO  @ Fri, 06 Jan 2017 15:26:56:  42000000 
INFO  @ Fri, 06 Jan 2017 15:27:04:  43000000 
INFO  @ Fri, 06 Jan 2017 15:27:12:  44000000 
INFO  @ Fri, 06 Jan 2017 15:27:19:  45000000 
INFO  @ Fri, 06 Jan 2017 15:27:27:  46000000 
INFO  @ Fri, 06 Jan 2017 15:27:34:  47000000 
INFO  @ Fri, 06 Jan 2017 15:27:42:  48000000 
INFO  @ Fri, 06 Jan 2017 15:27:49:  49000000 
INFO  @ Fri, 06 Jan 2017 15:27:56:  50000000 
INFO  @ Fri, 06 Jan 2017 15:28:00: #1 tag size is determined as 49 bps 
INFO  @ Fri, 06 Jan 2017 15:28:00: #1 tag size = 49 
INFO  @ Fri, 06 Jan 2017 15:28:00: #1  total tags in treatment: 20891566 
INFO  @ Fri, 06 Jan 2017 15:28:00: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:28:00: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:28:00: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:28:00: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:28:00: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:28:00: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:28:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:28:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:37:25: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:45:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.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/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:46:19: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:46:29: Done! 
INFO  @ Fri, 06 Jan 2017 15:46:56: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:50:00: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:57:54: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:00:49: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:25:25: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:37:09: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:56:14: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:59:04: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 17:06:00: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 17:08:30: Values in your input bedGraph files will be multiplied by 20.891566 ... 
INFO  @ Fri, 06 Jan 2017 17:31:58: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:34:19: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:47:07: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/rep1/SRR1370894_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	24267

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

Start	2017-01-06 14:37:13
End	2017-01-08 12:48:19
Elapsed	1 day 22:11:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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--------------------
35904 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign.gz 
opened /tmp/24267.1.amd.q/RtmpgOZt3j/SRR1370894_1.nodup.pr1.tagAlign8d0525526ae2
done. read 10445783 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24267.1.amd.q/RtmpgOZt3j/input15MReadsNSCLess1.05.50MSubsample.tagAlign8d056d5b5fc9
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1262155 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.155435345269383 
Top 3 estimates for fragment length 160 
Window half size 305 
Phantom peak location 55 
Phantom peak Correlation 0.1418189 
Normalized Strand cross-correlation coefficient (NSC) 1.231507 
Relative Strand cross-correlation Coefficient (RSC) 1.872667 
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= 5.010775  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1995699  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000187 
Detected 318813 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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL383555.2	198583	198887	.	0	.	38.5443122022411	-1	4.40186560719961	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL383555.2	198583	198887	.	0	.	38.5443122022411	-1	4.40186560719961	152

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24268

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

Start	2017-01-06 14:37:13
End	2017-01-08 11:42:49
Elapsed	1 day 21:05:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2 -speak=160 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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--------------------
35903 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 160 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign.gz 
opened /tmp/24268.1.amd.q/RtmpRkAtFx/SRR1370894_1.nodup.pr2.tagAlign8cf9422eed72
done. read 10445783 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24268.1.amd.q/RtmpRkAtFx/input15MReadsNSCLess1.05.50MSubsample.tagAlign8cf9144a01f
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1259937 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.155409318776509 
Top 3 estimates for fragment length 160 
Window half size 305 
Phantom peak location 55 
Phantom peak Correlation 0.1414856 
Normalized Strand cross-correlation coefficient (NSC) 1.233469 
Relative Strand cross-correlation Coefficient (RSC) 1.898773 
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= 5.011703  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.199533  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000055 
Detected 318115 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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	99329	99633	.	0	.	43.0775772343667	-1	4.47320951691359	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	99329	99633	.	0	.	43.0775772343667	-1	4.47320951691359	152

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24269

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

Start	2017-01-06 14:37:14
End	2017-01-06 15:40:49
Elapsed	01:03:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_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--------------------
35905 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:37:45: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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 14:37:45: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:37:45: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:37:52:  1000000 
INFO  @ Fri, 06 Jan 2017 14:37:58:  2000000 
INFO  @ Fri, 06 Jan 2017 14:38:04:  3000000 
INFO  @ Fri, 06 Jan 2017 14:38:11:  4000000 
INFO  @ Fri, 06 Jan 2017 14:38:17:  5000000 
INFO  @ Fri, 06 Jan 2017 14:38:24:  6000000 
INFO  @ Fri, 06 Jan 2017 14:38:30:  7000000 
INFO  @ Fri, 06 Jan 2017 14:38:37:  8000000 
INFO  @ Fri, 06 Jan 2017 14:38:43:  9000000 
INFO  @ Fri, 06 Jan 2017 14:38:50:  10000000 
INFO  @ Fri, 06 Jan 2017 14:38:54: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:39:00:  1000000 
INFO  @ Fri, 06 Jan 2017 14:39:06:  2000000 
INFO  @ Fri, 06 Jan 2017 14:39:13:  3000000 
INFO  @ Fri, 06 Jan 2017 14:39:19:  4000000 
INFO  @ Fri, 06 Jan 2017 14:39:26:  5000000 
INFO  @ Fri, 06 Jan 2017 14:39:32:  6000000 
INFO  @ Fri, 06 Jan 2017 14:39:38:  7000000 
INFO  @ Fri, 06 Jan 2017 14:39:45:  8000000 
INFO  @ Fri, 06 Jan 2017 14:39:51:  9000000 
INFO  @ Fri, 06 Jan 2017 14:39:57:  10000000 
INFO  @ Fri, 06 Jan 2017 14:40:04:  11000000 
INFO  @ Fri, 06 Jan 2017 14:40:10:  12000000 
INFO  @ Fri, 06 Jan 2017 14:40:17:  13000000 
INFO  @ Fri, 06 Jan 2017 14:40:24:  14000000 
INFO  @ Fri, 06 Jan 2017 14:40:31:  15000000 
INFO  @ Fri, 06 Jan 2017 14:40:38:  16000000 
INFO  @ Fri, 06 Jan 2017 14:40:44:  17000000 
INFO  @ Fri, 06 Jan 2017 14:40:51:  18000000 
INFO  @ Fri, 06 Jan 2017 14:40:58:  19000000 
INFO  @ Fri, 06 Jan 2017 14:41:05:  20000000 
INFO  @ Fri, 06 Jan 2017 14:41:11:  21000000 
INFO  @ Fri, 06 Jan 2017 14:41:19:  22000000 
INFO  @ Fri, 06 Jan 2017 14:41:25:  23000000 
INFO  @ Fri, 06 Jan 2017 14:41:32:  24000000 
INFO  @ Fri, 06 Jan 2017 14:41:39:  25000000 
INFO  @ Fri, 06 Jan 2017 14:41:47:  26000000 
INFO  @ Fri, 06 Jan 2017 14:41:54:  27000000 
INFO  @ Fri, 06 Jan 2017 14:42:01:  28000000 
INFO  @ Fri, 06 Jan 2017 14:42:08:  29000000 
INFO  @ Fri, 06 Jan 2017 14:42:16:  30000000 
INFO  @ Fri, 06 Jan 2017 14:42:24:  31000000 
INFO  @ Fri, 06 Jan 2017 14:42:31:  32000000 
INFO  @ Fri, 06 Jan 2017 14:42:39:  33000000 
INFO  @ Fri, 06 Jan 2017 14:42:47:  34000000 
INFO  @ Fri, 06 Jan 2017 14:42:55:  35000000 
INFO  @ Fri, 06 Jan 2017 14:43:03:  36000000 
INFO  @ Fri, 06 Jan 2017 14:43:10:  37000000 
INFO  @ Fri, 06 Jan 2017 14:43:18:  38000000 
INFO  @ Fri, 06 Jan 2017 14:43:26:  39000000 
INFO  @ Fri, 06 Jan 2017 14:43:34:  40000000 
INFO  @ Fri, 06 Jan 2017 14:43:42:  41000000 
INFO  @ Fri, 06 Jan 2017 14:43:49:  42000000 
INFO  @ Fri, 06 Jan 2017 14:43:57:  43000000 
INFO  @ Fri, 06 Jan 2017 14:44:05:  44000000 
INFO  @ Fri, 06 Jan 2017 14:44:13:  45000000 
INFO  @ Fri, 06 Jan 2017 14:44:21:  46000000 
INFO  @ Fri, 06 Jan 2017 14:44:29:  47000000 
INFO  @ Fri, 06 Jan 2017 14:44:37:  48000000 
INFO  @ Fri, 06 Jan 2017 14:44:45:  49000000 
INFO  @ Fri, 06 Jan 2017 14:44:53:  50000000 
INFO  @ Fri, 06 Jan 2017 14:44:57: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:44:57: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:44:57: #1  total tags in treatment: 10445783 
INFO  @ Fri, 06 Jan 2017 14:44:57: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:44:57: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:44:57: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:44:57: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:44:57: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:44:57: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:44:57: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:44:57: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:54:16: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:54:16: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:54:16: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:54:16: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:54:16: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:14:43: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:14:48: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:14:51: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:14:53: Done! 
INFO  @ Fri, 06 Jan 2017 15:15:03: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr1/SRR1370894_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 15:15:03: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:15:03: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:15:10:  1000000 
INFO  @ Fri, 06 Jan 2017 15:15:18:  2000000 
INFO  @ Fri, 06 Jan 2017 15:15:25:  3000000 
INFO  @ Fri, 06 Jan 2017 15:15:33:  4000000 
INFO  @ Fri, 06 Jan 2017 15:15:40:  5000000 
INFO  @ Fri, 06 Jan 2017 15:15:47:  6000000 
INFO  @ Fri, 06 Jan 2017 15:15:55:  7000000 
INFO  @ Fri, 06 Jan 2017 15:16:02:  8000000 
INFO  @ Fri, 06 Jan 2017 15:16:10:  9000000 
INFO  @ Fri, 06 Jan 2017 15:16:17:  10000000 
INFO  @ Fri, 06 Jan 2017 15:16:22: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:16:29:  1000000 
INFO  @ Fri, 06 Jan 2017 15:16:36:  2000000 
INFO  @ Fri, 06 Jan 2017 15:16:45:  3000000 
INFO  @ Fri, 06 Jan 2017 15:16:52:  4000000 
INFO  @ Fri, 06 Jan 2017 15:16:59:  5000000 
INFO  @ Fri, 06 Jan 2017 15:17:07:  6000000 
INFO  @ Fri, 06 Jan 2017 15:17:15:  7000000 
INFO  @ Fri, 06 Jan 2017 15:17:22:  8000000 
INFO  @ Fri, 06 Jan 2017 15:17:30:  9000000 
INFO  @ Fri, 06 Jan 2017 15:17:37:  10000000 
INFO  @ Fri, 06 Jan 2017 15:17:45:  11000000 
INFO  @ Fri, 06 Jan 2017 15:17:52:  12000000 
INFO  @ Fri, 06 Jan 2017 15:17:59:  13000000 
INFO  @ Fri, 06 Jan 2017 15:18:07:  14000000 
INFO  @ Fri, 06 Jan 2017 15:18:14:  15000000 
INFO  @ Fri, 06 Jan 2017 15:18:22:  16000000 
INFO  @ Fri, 06 Jan 2017 15:18:29:  17000000 
INFO  @ Fri, 06 Jan 2017 15:18:37:  18000000 
INFO  @ Fri, 06 Jan 2017 15:18:44:  19000000 
INFO  @ Fri, 06 Jan 2017 15:18:52:  20000000 
INFO  @ Fri, 06 Jan 2017 15:18:59:  21000000 
INFO  @ Fri, 06 Jan 2017 15:19:06:  22000000 
INFO  @ Fri, 06 Jan 2017 15:19:14:  23000000 
INFO  @ Fri, 06 Jan 2017 15:19:21:  24000000 
INFO  @ Fri, 06 Jan 2017 15:19:28:  25000000 
INFO  @ Fri, 06 Jan 2017 15:19:36:  26000000 
INFO  @ Fri, 06 Jan 2017 15:19:43:  27000000 
INFO  @ Fri, 06 Jan 2017 15:19:51:  28000000 
INFO  @ Fri, 06 Jan 2017 15:19:58:  29000000 
INFO  @ Fri, 06 Jan 2017 15:20:05:  30000000 
INFO  @ Fri, 06 Jan 2017 15:20:13:  31000000 
INFO  @ Fri, 06 Jan 2017 15:20:20:  32000000 
INFO  @ Fri, 06 Jan 2017 15:20:28:  33000000 
INFO  @ Fri, 06 Jan 2017 15:20:35:  34000000 
INFO  @ Fri, 06 Jan 2017 15:20:43:  35000000 
INFO  @ Fri, 06 Jan 2017 15:20:50:  36000000 
INFO  @ Fri, 06 Jan 2017 15:20:58:  37000000 
INFO  @ Fri, 06 Jan 2017 15:21:05:  38000000 
INFO  @ Fri, 06 Jan 2017 15:21:12:  39000000 
INFO  @ Fri, 06 Jan 2017 15:21:19:  40000000 
INFO  @ Fri, 06 Jan 2017 15:21:28:  41000000 
INFO  @ Fri, 06 Jan 2017 15:21:35:  42000000 
INFO  @ Fri, 06 Jan 2017 15:21:42:  43000000 
INFO  @ Fri, 06 Jan 2017 15:21:51:  44000000 
INFO  @ Fri, 06 Jan 2017 15:21:59:  45000000 
INFO  @ Fri, 06 Jan 2017 15:22:07:  46000000 
INFO  @ Fri, 06 Jan 2017 15:22:15:  47000000 
INFO  @ Fri, 06 Jan 2017 15:22:23:  48000000 
INFO  @ Fri, 06 Jan 2017 15:22:31:  49000000 
INFO  @ Fri, 06 Jan 2017 15:22:39:  50000000 
INFO  @ Fri, 06 Jan 2017 15:22:43: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:22:43: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:22:43: #1  total tags in treatment: 10445783 
INFO  @ Fri, 06 Jan 2017 15:22:43: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:22:43: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:22:43: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:22:43: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:22:43: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:22:43: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:22:43: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:22:43: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:31:44: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:39:30: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:39:51: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:40:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:40:18: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24334

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

Start	2017-01-06 15:40:52
End	2017-01-06 16:00:04
Elapsed	00:19:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_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--------------------
9896 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:41:09: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 160 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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 15:41:09: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:41:09: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:41:12:  1000000 
INFO  @ Fri, 06 Jan 2017 15:41:14:  2000000 
INFO  @ Fri, 06 Jan 2017 15:41:15:  3000000 
INFO  @ Fri, 06 Jan 2017 15:41:17:  4000000 
INFO  @ Fri, 06 Jan 2017 15:41:19:  5000000 
INFO  @ Fri, 06 Jan 2017 15:41:21:  6000000 
INFO  @ Fri, 06 Jan 2017 15:41:23:  7000000 
INFO  @ Fri, 06 Jan 2017 15:41:24:  8000000 
INFO  @ Fri, 06 Jan 2017 15:41:26:  9000000 
INFO  @ Fri, 06 Jan 2017 15:41:28:  10000000 
INFO  @ Fri, 06 Jan 2017 15:41:29: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:41:31:  1000000 
INFO  @ Fri, 06 Jan 2017 15:41:33:  2000000 
INFO  @ Fri, 06 Jan 2017 15:41:35:  3000000 
INFO  @ Fri, 06 Jan 2017 15:41:37:  4000000 
INFO  @ Fri, 06 Jan 2017 15:41:39:  5000000 
INFO  @ Fri, 06 Jan 2017 15:41:41:  6000000 
INFO  @ Fri, 06 Jan 2017 15:41:42:  7000000 
INFO  @ Fri, 06 Jan 2017 15:41:45:  8000000 
INFO  @ Fri, 06 Jan 2017 15:41:47:  9000000 
INFO  @ Fri, 06 Jan 2017 15:41:49:  10000000 
INFO  @ Fri, 06 Jan 2017 15:41:51:  11000000 
INFO  @ Fri, 06 Jan 2017 15:41:53:  12000000 
INFO  @ Fri, 06 Jan 2017 15:41:55:  13000000 
INFO  @ Fri, 06 Jan 2017 15:41:57:  14000000 
INFO  @ Fri, 06 Jan 2017 15:41:59:  15000000 
INFO  @ Fri, 06 Jan 2017 15:42:01:  16000000 
INFO  @ Fri, 06 Jan 2017 15:42:03:  17000000 
INFO  @ Fri, 06 Jan 2017 15:42:05:  18000000 
INFO  @ Fri, 06 Jan 2017 15:42:06:  19000000 
INFO  @ Fri, 06 Jan 2017 15:42:08:  20000000 
INFO  @ Fri, 06 Jan 2017 15:42:10:  21000000 
INFO  @ Fri, 06 Jan 2017 15:42:12:  22000000 
INFO  @ Fri, 06 Jan 2017 15:42:13:  23000000 
INFO  @ Fri, 06 Jan 2017 15:42:15:  24000000 
INFO  @ Fri, 06 Jan 2017 15:42:16:  25000000 
INFO  @ Fri, 06 Jan 2017 15:42:18:  26000000 
INFO  @ Fri, 06 Jan 2017 15:42:20:  27000000 
INFO  @ Fri, 06 Jan 2017 15:42:21:  28000000 
INFO  @ Fri, 06 Jan 2017 15:42:23:  29000000 
INFO  @ Fri, 06 Jan 2017 15:42:25:  30000000 
INFO  @ Fri, 06 Jan 2017 15:42:26:  31000000 
INFO  @ Fri, 06 Jan 2017 15:42:28:  32000000 
INFO  @ Fri, 06 Jan 2017 15:42:30:  33000000 
INFO  @ Fri, 06 Jan 2017 15:42:32:  34000000 
INFO  @ Fri, 06 Jan 2017 15:42:35:  35000000 
INFO  @ Fri, 06 Jan 2017 15:42:36:  36000000 
INFO  @ Fri, 06 Jan 2017 15:42:38:  37000000 
INFO  @ Fri, 06 Jan 2017 15:42:40:  38000000 
INFO  @ Fri, 06 Jan 2017 15:42:41:  39000000 
INFO  @ Fri, 06 Jan 2017 15:42:43:  40000000 
INFO  @ Fri, 06 Jan 2017 15:42:45:  41000000 
INFO  @ Fri, 06 Jan 2017 15:42:46:  42000000 
INFO  @ Fri, 06 Jan 2017 15:42:48:  43000000 
INFO  @ Fri, 06 Jan 2017 15:42:50:  44000000 
INFO  @ Fri, 06 Jan 2017 15:42:52:  45000000 
INFO  @ Fri, 06 Jan 2017 15:42:54:  46000000 
INFO  @ Fri, 06 Jan 2017 15:42:55:  47000000 
INFO  @ Fri, 06 Jan 2017 15:42:57:  48000000 
INFO  @ Fri, 06 Jan 2017 15:42:59:  49000000 
INFO  @ Fri, 06 Jan 2017 15:43:01:  50000000 
INFO  @ Fri, 06 Jan 2017 15:43:03: #1 tag size is determined as 49 bps 
INFO  @ Fri, 06 Jan 2017 15:43:03: #1 tag size = 49 
INFO  @ Fri, 06 Jan 2017 15:43:03: #1  total tags in treatment: 10445783 
INFO  @ Fri, 06 Jan 2017 15:43:03: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:43:03: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:43:03: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:43:03: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:43:03: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:43:03: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:43:03: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:43:03: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:46:01: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:46:01: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:46:01: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:46:01: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:46:01: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:51:23: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:51:24: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:51:25: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:51:26: Done! 
INFO  @ Fri, 06 Jan 2017 15:51:29: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 160 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/pseudo_reps/rep1/pr2/SRR1370894_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 15:51:29: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:51:29: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:51:31:  1000000 
INFO  @ Fri, 06 Jan 2017 15:51:33:  2000000 
INFO  @ Fri, 06 Jan 2017 15:51:34:  3000000 
INFO  @ Fri, 06 Jan 2017 15:51:36:  4000000 
INFO  @ Fri, 06 Jan 2017 15:51:38:  5000000 
INFO  @ Fri, 06 Jan 2017 15:51:39:  6000000 
INFO  @ Fri, 06 Jan 2017 15:51:41:  7000000 
INFO  @ Fri, 06 Jan 2017 15:51:43:  8000000 
INFO  @ Fri, 06 Jan 2017 15:51:45:  9000000 
INFO  @ Fri, 06 Jan 2017 15:51:47:  10000000 
INFO  @ Fri, 06 Jan 2017 15:51:48: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:51:50:  1000000 
INFO  @ Fri, 06 Jan 2017 15:51:52:  2000000 
INFO  @ Fri, 06 Jan 2017 15:51:54:  3000000 
INFO  @ Fri, 06 Jan 2017 15:51:56:  4000000 
INFO  @ Fri, 06 Jan 2017 15:51:57:  5000000 
INFO  @ Fri, 06 Jan 2017 15:51:59:  6000000 
INFO  @ Fri, 06 Jan 2017 15:52:01:  7000000 
INFO  @ Fri, 06 Jan 2017 15:52:02:  8000000 
INFO  @ Fri, 06 Jan 2017 15:52:04:  9000000 
INFO  @ Fri, 06 Jan 2017 15:52:06:  10000000 
INFO  @ Fri, 06 Jan 2017 15:52:08:  11000000 
INFO  @ Fri, 06 Jan 2017 15:52:10:  12000000 
INFO  @ Fri, 06 Jan 2017 15:52:11:  13000000 
INFO  @ Fri, 06 Jan 2017 15:52:13:  14000000 
INFO  @ Fri, 06 Jan 2017 15:52:14:  15000000 
INFO  @ Fri, 06 Jan 2017 15:52:16:  16000000 
INFO  @ Fri, 06 Jan 2017 15:52:18:  17000000 
INFO  @ Fri, 06 Jan 2017 15:52:20:  18000000 
INFO  @ Fri, 06 Jan 2017 15:52:21:  19000000 
INFO  @ Fri, 06 Jan 2017 15:52:23:  20000000 
INFO  @ Fri, 06 Jan 2017 15:52:24:  21000000 
INFO  @ Fri, 06 Jan 2017 15:52:26:  22000000 
INFO  @ Fri, 06 Jan 2017 15:52:28:  23000000 
INFO  @ Fri, 06 Jan 2017 15:52:30:  24000000 
INFO  @ Fri, 06 Jan 2017 15:52:31:  25000000 
INFO  @ Fri, 06 Jan 2017 15:52:33:  26000000 
INFO  @ Fri, 06 Jan 2017 15:52:35:  27000000 
INFO  @ Fri, 06 Jan 2017 15:52:37:  28000000 
INFO  @ Fri, 06 Jan 2017 15:52:38:  29000000 
INFO  @ Fri, 06 Jan 2017 15:52:40:  30000000 
INFO  @ Fri, 06 Jan 2017 15:52:42:  31000000 
INFO  @ Fri, 06 Jan 2017 15:52:44:  32000000 
INFO  @ Fri, 06 Jan 2017 15:52:45:  33000000 
INFO  @ Fri, 06 Jan 2017 15:52:47:  34000000 
INFO  @ Fri, 06 Jan 2017 15:52:49:  35000000 
INFO  @ Fri, 06 Jan 2017 15:52:51:  36000000 
INFO  @ Fri, 06 Jan 2017 15:52:52:  37000000 
INFO  @ Fri, 06 Jan 2017 15:52:54:  38000000 
INFO  @ Fri, 06 Jan 2017 15:52:56:  39000000 
INFO  @ Fri, 06 Jan 2017 15:52:57:  40000000 
INFO  @ Fri, 06 Jan 2017 15:52:59:  41000000 
INFO  @ Fri, 06 Jan 2017 15:53:01:  42000000 
INFO  @ Fri, 06 Jan 2017 15:53:02:  43000000 
INFO  @ Fri, 06 Jan 2017 15:53:04:  44000000 
INFO  @ Fri, 06 Jan 2017 15:53:06:  45000000 
INFO  @ Fri, 06 Jan 2017 15:53:08:  46000000 
INFO  @ Fri, 06 Jan 2017 15:53:09:  47000000 
INFO  @ Fri, 06 Jan 2017 15:53:11:  48000000 
INFO  @ Fri, 06 Jan 2017 15:53:13:  49000000 
INFO  @ Fri, 06 Jan 2017 15:53:15:  50000000 
INFO  @ Fri, 06 Jan 2017 15:53:17: #1 tag size is determined as 49 bps 
INFO  @ Fri, 06 Jan 2017 15:53:17: #1 tag size = 49 
INFO  @ Fri, 06 Jan 2017 15:53:17: #1  total tags in treatment: 10445783 
INFO  @ Fri, 06 Jan 2017 15:53:17: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:53:17: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:53:17: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:53:17: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:53:17: #2 Use 160 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:53:17: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:53:17: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:53:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:56:52: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:59:35: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:59:41: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:59:45: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:59:50: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24565

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

Start	2017-01-08 18:10:10
End	2017-01-08 18:11:22
Elapsed	00:01:12
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_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--------------------
11055 (process ID) old priority 0, new priority 10
Waiting for 54 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL383555.2	198583	198887	.	0	.	38.5443122022411	-1	4.40186560719961	152

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL383555.2	198583	198887	.	0	.	38.5443122022411	-1	4.40186560719961	152

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000219.1	99329	99633	.	0	.	43.0775772343667	-1	4.47320951691359	152

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000219.1	99329	99633	.	0	.	43.0775772343667	-1	4.47320951691359	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	68253	68557	.	0	.	10.7997919864641	-1	3.86070187811448	152

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	68253	68557	.	0	.	10.7997919864641	-1	3.86070187811448	152

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24566

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

Start	2017-01-08 18:11:23
End	2017-01-08 18:14:25
Elapsed	00:03:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370894_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370894_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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--------------------
11154 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.70 1.28 0.87 0.47]
Number of reported peaks - 91868/91868 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 29327/91868 (31.9%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24567

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

Start	2017-01-08 18:14:27
End	2017-01-08 18:15:37
Elapsed	00:01:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/qc/ZNF322_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/ZNF322/out/qc/ZNF322_IDR_final.qc

# SYS command. line 224

 echo -e "0\t917	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/qc/ZNF322_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--------------------
11280 (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	39762

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

Start	2017-01-08 18:15:39
End	2017-01-08 18:16:48
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_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/ZNF322/out/peak/spp/rep1/SRR1370894_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--------------------
39766 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	99419	99581	.	0	.	76.7788412093407	-1	4.46898205896257	73

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/rep1/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
GL000219.1	99419	99581	.	0	.	76.7788412093407	-1	4.46898205896257	73

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	43429

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

Start	2017-01-08 18:16:49
End	2017-01-08 18:16:57
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/spp/overlap/SRR1370894_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/ZNF322/out/peak/spp/overlap/SRR1370894_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
43434 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	43958

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

Start	2017-01-08 18:16:58
End	2017-01-08 18:17:07
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_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/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/peak/idr/pseudo_reps/rep1/ZNF322_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
43964 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	44548

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

Start	2017-01-08 18:17:08
End	2017-01-08 18:17:16
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/ZNF322/out/report/ZNF322_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/report/ZNF322_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/report/ZNF322_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
44552 (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, ZNF322, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF322/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF322/out/align/rep1/SRR1370894_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/ZNF322
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/ZNF322
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	55063.ZNF322.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