Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_144731_189
Start time	2017-01-06 14:47:31
Run time	22:14:30.751
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZSCAN31, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZSCAN31/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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_144731_189/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_144731_189/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_144731_189/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_144731_189/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_144731_189/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_144731_189/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_144731_189/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_144731_189/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_144731_189/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_144731_189/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_144731_189/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_144731_189/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_144731_189/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	24313

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

Start	2017-01-06 14:47:38
End	2017-01-07 12:56:35
Elapsed	22:08:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_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--------------------
31737 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_1.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 150 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/align/rep1/SRR1370896_1.nodup.tagAlign.gz 
opened /tmp/24313.1.q/RtmpQIz7H9/SRR1370896_1.nodup.tagAlign7c3f26af36a2
done. read 17610831 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/24313.1.q/RtmpQIz7H9/input15MReadsNSCLess1.05.50MSubsample.tagAlign7c3f34ccbc14
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1988589 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.204782700038334 
Top 3 estimates for fragment length 150 
Window half size 270 
Phantom peak location 50 
Phantom peak Correlation 0.2024893 
Normalized Strand cross-correlation coefficient (NSC) 1.029789 
Relative Strand cross-correlation Coefficient (RSC) 1.631718 
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= 2.842118  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.3518503  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000012 
Detected 602358 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/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196483.1	11507	11777	.	0	.	22.5787461209494	-1	3.50219944265838	135

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196483.1	11507	11777	.	0	.	22.5787461209494	-1	3.50219944265838	135

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24314

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

Start	2017-01-06 14:47:38
End	2017-01-06 16:13:07
Elapsed	01:25:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/signal/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/signal/macs2/rep1/SRR1370896_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/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1 -o "SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/signal/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1 -o "SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/signal/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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--------------------
7211 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:11:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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 15:11:53: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:11:53: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:11:55:  1000000 
INFO  @ Fri, 06 Jan 2017 15:11:56:  2000000 
INFO  @ Fri, 06 Jan 2017 15:11:58:  3000000 
INFO  @ Fri, 06 Jan 2017 15:12:00:  4000000 
INFO  @ Fri, 06 Jan 2017 15:12:01:  5000000 
INFO  @ Fri, 06 Jan 2017 15:12:03:  6000000 
INFO  @ Fri, 06 Jan 2017 15:12:05:  7000000 
INFO  @ Fri, 06 Jan 2017 15:12:06:  8000000 
INFO  @ Fri, 06 Jan 2017 15:12:08:  9000000 
INFO  @ Fri, 06 Jan 2017 15:12:09:  10000000 
INFO  @ Fri, 06 Jan 2017 15:12:11:  11000000 
INFO  @ Fri, 06 Jan 2017 15:12:13:  12000000 
INFO  @ Fri, 06 Jan 2017 15:12:14:  13000000 
INFO  @ Fri, 06 Jan 2017 15:12:16:  14000000 
INFO  @ Fri, 06 Jan 2017 15:12:18:  15000000 
INFO  @ Fri, 06 Jan 2017 15:12:20:  16000000 
INFO  @ Fri, 06 Jan 2017 15:12:22:  17000000 
INFO  @ Fri, 06 Jan 2017 15:12:23: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:12:25:  1000000 
INFO  @ Fri, 06 Jan 2017 15:12:26:  2000000 
INFO  @ Fri, 06 Jan 2017 15:12:28:  3000000 
INFO  @ Fri, 06 Jan 2017 15:12:30:  4000000 
INFO  @ Fri, 06 Jan 2017 15:12:31:  5000000 
INFO  @ Fri, 06 Jan 2017 15:12:33:  6000000 
INFO  @ Fri, 06 Jan 2017 15:12:35:  7000000 
INFO  @ Fri, 06 Jan 2017 15:12:36:  8000000 
INFO  @ Fri, 06 Jan 2017 15:12:38:  9000000 
INFO  @ Fri, 06 Jan 2017 15:12:40:  10000000 
INFO  @ Fri, 06 Jan 2017 15:12:41:  11000000 
INFO  @ Fri, 06 Jan 2017 15:12:43:  12000000 
INFO  @ Fri, 06 Jan 2017 15:12:45:  13000000 
INFO  @ Fri, 06 Jan 2017 15:12:46:  14000000 
INFO  @ Fri, 06 Jan 2017 15:12:48:  15000000 
INFO  @ Fri, 06 Jan 2017 15:12:50:  16000000 
INFO  @ Fri, 06 Jan 2017 15:12:51:  17000000 
INFO  @ Fri, 06 Jan 2017 15:12:53:  18000000 
INFO  @ Fri, 06 Jan 2017 15:12:55:  19000000 
INFO  @ Fri, 06 Jan 2017 15:12:56:  20000000 
INFO  @ Fri, 06 Jan 2017 15:12:58:  21000000 
INFO  @ Fri, 06 Jan 2017 15:13:00:  22000000 
INFO  @ Fri, 06 Jan 2017 15:13:01:  23000000 
INFO  @ Fri, 06 Jan 2017 15:13:03:  24000000 
INFO  @ Fri, 06 Jan 2017 15:13:05:  25000000 
INFO  @ Fri, 06 Jan 2017 15:13:07:  26000000 
INFO  @ Fri, 06 Jan 2017 15:13:09:  27000000 
INFO  @ Fri, 06 Jan 2017 15:13:10:  28000000 
INFO  @ Fri, 06 Jan 2017 15:13:12:  29000000 
INFO  @ Fri, 06 Jan 2017 15:13:13:  30000000 
INFO  @ Fri, 06 Jan 2017 15:13:15:  31000000 
INFO  @ Fri, 06 Jan 2017 15:13:17:  32000000 
INFO  @ Fri, 06 Jan 2017 15:13:18:  33000000 
INFO  @ Fri, 06 Jan 2017 15:13:20:  34000000 
INFO  @ Fri, 06 Jan 2017 15:13:22:  35000000 
INFO  @ Fri, 06 Jan 2017 15:13:23:  36000000 
INFO  @ Fri, 06 Jan 2017 15:13:25:  37000000 
INFO  @ Fri, 06 Jan 2017 15:13:26:  38000000 
INFO  @ Fri, 06 Jan 2017 15:13:28:  39000000 
INFO  @ Fri, 06 Jan 2017 15:13:29:  40000000 
INFO  @ Fri, 06 Jan 2017 15:13:31:  41000000 
INFO  @ Fri, 06 Jan 2017 15:13:33:  42000000 
INFO  @ Fri, 06 Jan 2017 15:13:34:  43000000 
INFO  @ Fri, 06 Jan 2017 15:13:36:  44000000 
INFO  @ Fri, 06 Jan 2017 15:13:38:  45000000 
INFO  @ Fri, 06 Jan 2017 15:13:40:  46000000 
INFO  @ Fri, 06 Jan 2017 15:13:41:  47000000 
INFO  @ Fri, 06 Jan 2017 15:13:43:  48000000 
INFO  @ Fri, 06 Jan 2017 15:13:45:  49000000 
INFO  @ Fri, 06 Jan 2017 15:13:47:  50000000 
INFO  @ Fri, 06 Jan 2017 15:13:49: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:13:49: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:13:49: #1  total tags in treatment: 17610831 
INFO  @ Fri, 06 Jan 2017 15:13:49: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:13:49: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:13:49: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:13:49: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:13:49: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:13:49: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:13:49: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:13:49: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:16:58: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:16:58: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:16:58: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:16:58: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:16:58: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:22:26: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:22:28: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:22:28: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:22:29: Done! 
INFO  @ Fri, 06 Jan 2017 15:22:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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 15:22:31: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:22:31: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:22:34:  1000000 
INFO  @ Fri, 06 Jan 2017 15:22:36:  2000000 
INFO  @ Fri, 06 Jan 2017 15:22:37:  3000000 
INFO  @ Fri, 06 Jan 2017 15:22:39:  4000000 
INFO  @ Fri, 06 Jan 2017 15:22:41:  5000000 
INFO  @ Fri, 06 Jan 2017 15:22:43:  6000000 
INFO  @ Fri, 06 Jan 2017 15:22:45:  7000000 
INFO  @ Fri, 06 Jan 2017 15:22:46:  8000000 
INFO  @ Fri, 06 Jan 2017 15:22:48:  9000000 
INFO  @ Fri, 06 Jan 2017 15:22:49:  10000000 
INFO  @ Fri, 06 Jan 2017 15:22:51:  11000000 
INFO  @ Fri, 06 Jan 2017 15:22:53:  12000000 
INFO  @ Fri, 06 Jan 2017 15:22:55:  13000000 
INFO  @ Fri, 06 Jan 2017 15:22:56:  14000000 
INFO  @ Fri, 06 Jan 2017 15:22:58:  15000000 
INFO  @ Fri, 06 Jan 2017 15:22:59:  16000000 
INFO  @ Fri, 06 Jan 2017 15:23:01:  17000000 
INFO  @ Fri, 06 Jan 2017 15:23:02: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:23:04:  1000000 
INFO  @ Fri, 06 Jan 2017 15:23:06:  2000000 
INFO  @ Fri, 06 Jan 2017 15:23:08:  3000000 
INFO  @ Fri, 06 Jan 2017 15:23:10:  4000000 
INFO  @ Fri, 06 Jan 2017 15:23:11:  5000000 
INFO  @ Fri, 06 Jan 2017 15:23:13:  6000000 
INFO  @ Fri, 06 Jan 2017 15:23:15:  7000000 
INFO  @ Fri, 06 Jan 2017 15:23:17:  8000000 
INFO  @ Fri, 06 Jan 2017 15:23:18:  9000000 
INFO  @ Fri, 06 Jan 2017 15:23:20:  10000000 
INFO  @ Fri, 06 Jan 2017 15:23:22:  11000000 
INFO  @ Fri, 06 Jan 2017 15:23:23:  12000000 
INFO  @ Fri, 06 Jan 2017 15:23:25:  13000000 
INFO  @ Fri, 06 Jan 2017 15:23:26:  14000000 
INFO  @ Fri, 06 Jan 2017 15:23:28:  15000000 
INFO  @ Fri, 06 Jan 2017 15:23:29:  16000000 
INFO  @ Fri, 06 Jan 2017 15:23:31:  17000000 
INFO  @ Fri, 06 Jan 2017 15:23:33:  18000000 
INFO  @ Fri, 06 Jan 2017 15:23:34:  19000000 
INFO  @ Fri, 06 Jan 2017 15:23:36:  20000000 
INFO  @ Fri, 06 Jan 2017 15:23:37:  21000000 
INFO  @ Fri, 06 Jan 2017 15:23:39:  22000000 
INFO  @ Fri, 06 Jan 2017 15:23:41:  23000000 
INFO  @ Fri, 06 Jan 2017 15:23:42:  24000000 
INFO  @ Fri, 06 Jan 2017 15:23:44:  25000000 
INFO  @ Fri, 06 Jan 2017 15:23:45:  26000000 
INFO  @ Fri, 06 Jan 2017 15:23:47:  27000000 
INFO  @ Fri, 06 Jan 2017 15:23:48:  28000000 
INFO  @ Fri, 06 Jan 2017 15:23:50:  29000000 
INFO  @ Fri, 06 Jan 2017 15:23:52:  30000000 
INFO  @ Fri, 06 Jan 2017 15:23:54:  31000000 
INFO  @ Fri, 06 Jan 2017 15:23:56:  32000000 
INFO  @ Fri, 06 Jan 2017 15:23:57:  33000000 
INFO  @ Fri, 06 Jan 2017 15:23:59:  34000000 
INFO  @ Fri, 06 Jan 2017 15:24:02:  35000000 
INFO  @ Fri, 06 Jan 2017 15:24:04:  36000000 
INFO  @ Fri, 06 Jan 2017 15:24:05:  37000000 
INFO  @ Fri, 06 Jan 2017 15:24:07:  38000000 
INFO  @ Fri, 06 Jan 2017 15:24:10:  39000000 
INFO  @ Fri, 06 Jan 2017 15:24:12:  40000000 
INFO  @ Fri, 06 Jan 2017 15:24:14:  41000000 
INFO  @ Fri, 06 Jan 2017 15:24:16:  42000000 
INFO  @ Fri, 06 Jan 2017 15:24:18:  43000000 
INFO  @ Fri, 06 Jan 2017 15:24:20:  44000000 
INFO  @ Fri, 06 Jan 2017 15:24:22:  45000000 
INFO  @ Fri, 06 Jan 2017 15:24:25:  46000000 
INFO  @ Fri, 06 Jan 2017 15:24:27:  47000000 
INFO  @ Fri, 06 Jan 2017 15:24:29:  48000000 
INFO  @ Fri, 06 Jan 2017 15:24:31:  49000000 
INFO  @ Fri, 06 Jan 2017 15:24:32:  50000000 
INFO  @ Fri, 06 Jan 2017 15:24:34: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:24:34: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:24:34: #1  total tags in treatment: 17610831 
INFO  @ Fri, 06 Jan 2017 15:24:34: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:24:34: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:24:34: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:24:34: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:24:34: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:24:34: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:24:34: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:24:34: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:28:14: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:30:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:30:59: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:31:04: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:31:08: Done! 
INFO  @ Fri, 06 Jan 2017 15:31:21: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:32:01: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:33:47: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:34:40: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 15:39:52: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:43:18: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 15:50:42: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:51:21: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:53:06: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:54:08: Values in your input bedGraph files will be multiplied by 17.610831 ... 
INFO  @ Fri, 06 Jan 2017 15:59:49: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 16:00:29: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:03:32: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/rep1/SRR1370896_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	24315

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

Start	2017-01-06 14:47:39
End	2017-01-07 11:01:30
Elapsed	20:13:50
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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--------------------
31861 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 150 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign.gz 
opened /tmp/24315.1.q/RtmpiZemdA/SRR1370896_1.nodup.pr1.tagAlign7cb565f9c5ba
done. read 8805416 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/24315.1.q/RtmpiZemdA/input15MReadsNSCLess1.05.50MSubsample.tagAlign7cb53670e580
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1112442 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.114541867066726 
Top 3 estimates for fragment length 150 
Window half size 270 
Phantom peak location 50 
Phantom peak Correlation 0.113262 
Normalized Strand cross-correlation coefficient (NSC) 1.029643 
Relative Strand cross-correlation Coefficient (RSC) 1.634307 
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= 5.679028  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1760865  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000068 
Detected 229551 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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270733.1	168753	169023	.	0	.	15.2196396381056	-1	3.13192504997534	135

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270733.1	168753	169023	.	0	.	15.2196396381056	-1	3.13192504997534	135

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24316

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

Start	2017-01-06 14:47:40
End	2017-01-07 11:00:56
Elapsed	20:13:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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--------------------
31960 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 150 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign.gz 
opened /tmp/24316.1.q/RtmpLEvZfc/SRR1370896_1.nodup.pr2.tagAlign7d1b5c13894
done. read 8805415 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/24316.1.q/RtmpLEvZfc/input15MReadsNSCLess1.05.50MSubsample.tagAlign7d1b57863d27
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1106907 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.113987156382415 
Top 3 estimates for fragment length 150 
Window half size 275 
Phantom peak location 50 
Phantom peak Correlation 0.112717 
Normalized Strand cross-correlation coefficient (NSC) 1.029781 
Relative Strand cross-correlation Coefficient (RSC) 1.62684 
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= 5.678613  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1760993  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000252 
Detected 230486 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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196483.1	11504	11780	.	0	.	13.7278702175475	-1	3.44142279815339	138

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196483.1	11504	11780	.	0	.	13.7278702175475	-1	3.44142279815339	138

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24317

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

Start	2017-01-06 14:47:41
End	2017-01-06 15:35:44
Elapsed	00:48:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_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--------------------
7468 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:17:09: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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 15:17:09: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:17:09: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:17:11:  1000000 
INFO  @ Fri, 06 Jan 2017 15:17:13:  2000000 
INFO  @ Fri, 06 Jan 2017 15:17:15:  3000000 
INFO  @ Fri, 06 Jan 2017 15:17:16:  4000000 
INFO  @ Fri, 06 Jan 2017 15:17:18:  5000000 
INFO  @ Fri, 06 Jan 2017 15:17:20:  6000000 
INFO  @ Fri, 06 Jan 2017 15:17:21:  7000000 
INFO  @ Fri, 06 Jan 2017 15:17:23:  8000000 
INFO  @ Fri, 06 Jan 2017 15:17:25: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:17:27:  1000000 
INFO  @ Fri, 06 Jan 2017 15:17:29:  2000000 
INFO  @ Fri, 06 Jan 2017 15:17:31:  3000000 
INFO  @ Fri, 06 Jan 2017 15:17:32:  4000000 
INFO  @ Fri, 06 Jan 2017 15:17:34:  5000000 
INFO  @ Fri, 06 Jan 2017 15:17:36:  6000000 
INFO  @ Fri, 06 Jan 2017 15:17:37:  7000000 
INFO  @ Fri, 06 Jan 2017 15:17:39:  8000000 
INFO  @ Fri, 06 Jan 2017 15:17:40:  9000000 
INFO  @ Fri, 06 Jan 2017 15:17:42:  10000000 
INFO  @ Fri, 06 Jan 2017 15:17:44:  11000000 
INFO  @ Fri, 06 Jan 2017 15:17:46:  12000000 
INFO  @ Fri, 06 Jan 2017 15:17:47:  13000000 
INFO  @ Fri, 06 Jan 2017 15:17:49:  14000000 
INFO  @ Fri, 06 Jan 2017 15:17:50:  15000000 
INFO  @ Fri, 06 Jan 2017 15:17:52:  16000000 
INFO  @ Fri, 06 Jan 2017 15:17:54:  17000000 
INFO  @ Fri, 06 Jan 2017 15:17:56:  18000000 
INFO  @ Fri, 06 Jan 2017 15:17:57:  19000000 
INFO  @ Fri, 06 Jan 2017 15:17:59:  20000000 
INFO  @ Fri, 06 Jan 2017 15:18:01:  21000000 
INFO  @ Fri, 06 Jan 2017 15:18:02:  22000000 
INFO  @ Fri, 06 Jan 2017 15:18:04:  23000000 
INFO  @ Fri, 06 Jan 2017 15:18:06:  24000000 
INFO  @ Fri, 06 Jan 2017 15:18:08:  25000000 
INFO  @ Fri, 06 Jan 2017 15:18:09:  26000000 
INFO  @ Fri, 06 Jan 2017 15:18:11:  27000000 
INFO  @ Fri, 06 Jan 2017 15:18:13:  28000000 
INFO  @ Fri, 06 Jan 2017 15:18:15:  29000000 
INFO  @ Fri, 06 Jan 2017 15:18:16:  30000000 
INFO  @ Fri, 06 Jan 2017 15:18:18:  31000000 
INFO  @ Fri, 06 Jan 2017 15:18:20:  32000000 
INFO  @ Fri, 06 Jan 2017 15:18:21:  33000000 
INFO  @ Fri, 06 Jan 2017 15:18:23:  34000000 
INFO  @ Fri, 06 Jan 2017 15:18:25:  35000000 
INFO  @ Fri, 06 Jan 2017 15:18:27:  36000000 
INFO  @ Fri, 06 Jan 2017 15:18:28:  37000000 
INFO  @ Fri, 06 Jan 2017 15:18:30:  38000000 
INFO  @ Fri, 06 Jan 2017 15:18:31:  39000000 
INFO  @ Fri, 06 Jan 2017 15:18:33:  40000000 
INFO  @ Fri, 06 Jan 2017 15:18:35:  41000000 
INFO  @ Fri, 06 Jan 2017 15:18:37:  42000000 
INFO  @ Fri, 06 Jan 2017 15:18:38:  43000000 
INFO  @ Fri, 06 Jan 2017 15:18:40:  44000000 
INFO  @ Fri, 06 Jan 2017 15:18:42:  45000000 
INFO  @ Fri, 06 Jan 2017 15:18:44:  46000000 
INFO  @ Fri, 06 Jan 2017 15:18:45:  47000000 
INFO  @ Fri, 06 Jan 2017 15:18:47:  48000000 
INFO  @ Fri, 06 Jan 2017 15:18:49:  49000000 
INFO  @ Fri, 06 Jan 2017 15:18:50:  50000000 
INFO  @ Fri, 06 Jan 2017 15:18:52: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:18:52: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:18:52: #1  total tags in treatment: 8805416 
INFO  @ Fri, 06 Jan 2017 15:18:52: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:18:52: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:18:52: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:18:52: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:18:52: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:18:52: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:18:52: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:18:52: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:21:59: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:21:59: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:21:59: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:21:59: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:21:59: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:27:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:27:09: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:27:10: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:27:10: Done! 
INFO  @ Fri, 06 Jan 2017 15:27:14: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr1/SRR1370896_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 15:27:14: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:27:14: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:27:16:  1000000 
INFO  @ Fri, 06 Jan 2017 15:27:18:  2000000 
INFO  @ Fri, 06 Jan 2017 15:27:21:  3000000 
INFO  @ Fri, 06 Jan 2017 15:27:23:  4000000 
INFO  @ Fri, 06 Jan 2017 15:27:25:  5000000 
INFO  @ Fri, 06 Jan 2017 15:27:27:  6000000 
INFO  @ Fri, 06 Jan 2017 15:27:29:  7000000 
INFO  @ Fri, 06 Jan 2017 15:27:32:  8000000 
INFO  @ Fri, 06 Jan 2017 15:27:34: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:27:36:  1000000 
INFO  @ Fri, 06 Jan 2017 15:27:38:  2000000 
INFO  @ Fri, 06 Jan 2017 15:27:40:  3000000 
INFO  @ Fri, 06 Jan 2017 15:27:43:  4000000 
INFO  @ Fri, 06 Jan 2017 15:27:44:  5000000 
INFO  @ Fri, 06 Jan 2017 15:27:46:  6000000 
INFO  @ Fri, 06 Jan 2017 15:27:47:  7000000 
INFO  @ Fri, 06 Jan 2017 15:27:49:  8000000 
INFO  @ Fri, 06 Jan 2017 15:27:51:  9000000 
INFO  @ Fri, 06 Jan 2017 15:27:53:  10000000 
INFO  @ Fri, 06 Jan 2017 15:27:56:  11000000 
INFO  @ Fri, 06 Jan 2017 15:27:57:  12000000 
INFO  @ Fri, 06 Jan 2017 15:28:00:  13000000 
INFO  @ Fri, 06 Jan 2017 15:28:02:  14000000 
INFO  @ Fri, 06 Jan 2017 15:28:04:  15000000 
INFO  @ Fri, 06 Jan 2017 15:28:06:  16000000 
INFO  @ Fri, 06 Jan 2017 15:28:08:  17000000 
INFO  @ Fri, 06 Jan 2017 15:28:10:  18000000 
INFO  @ Fri, 06 Jan 2017 15:28:11:  19000000 
INFO  @ Fri, 06 Jan 2017 15:28:13:  20000000 
INFO  @ Fri, 06 Jan 2017 15:28:14:  21000000 
INFO  @ Fri, 06 Jan 2017 15:28:16:  22000000 
INFO  @ Fri, 06 Jan 2017 15:28:17:  23000000 
INFO  @ Fri, 06 Jan 2017 15:28:19:  24000000 
INFO  @ Fri, 06 Jan 2017 15:28:21:  25000000 
INFO  @ Fri, 06 Jan 2017 15:28:23:  26000000 
INFO  @ Fri, 06 Jan 2017 15:28:24:  27000000 
INFO  @ Fri, 06 Jan 2017 15:28:26:  28000000 
INFO  @ Fri, 06 Jan 2017 15:28:28:  29000000 
INFO  @ Fri, 06 Jan 2017 15:28:30:  30000000 
INFO  @ Fri, 06 Jan 2017 15:28:31:  31000000 
INFO  @ Fri, 06 Jan 2017 15:28:33:  32000000 
INFO  @ Fri, 06 Jan 2017 15:28:35:  33000000 
INFO  @ Fri, 06 Jan 2017 15:28:37:  34000000 
INFO  @ Fri, 06 Jan 2017 15:28:38:  35000000 
INFO  @ Fri, 06 Jan 2017 15:28:40:  36000000 
INFO  @ Fri, 06 Jan 2017 15:28:42:  37000000 
INFO  @ Fri, 06 Jan 2017 15:28:44:  38000000 
INFO  @ Fri, 06 Jan 2017 15:28:45:  39000000 
INFO  @ Fri, 06 Jan 2017 15:28:47:  40000000 
INFO  @ Fri, 06 Jan 2017 15:28:49:  41000000 
INFO  @ Fri, 06 Jan 2017 15:28:50:  42000000 
INFO  @ Fri, 06 Jan 2017 15:28:52:  43000000 
INFO  @ Fri, 06 Jan 2017 15:28:53:  44000000 
INFO  @ Fri, 06 Jan 2017 15:28:54:  45000000 
INFO  @ Fri, 06 Jan 2017 15:28:56:  46000000 
INFO  @ Fri, 06 Jan 2017 15:28:58:  47000000 
INFO  @ Fri, 06 Jan 2017 15:28:59:  48000000 
INFO  @ Fri, 06 Jan 2017 15:29:01:  49000000 
INFO  @ Fri, 06 Jan 2017 15:29:02:  50000000 
INFO  @ Fri, 06 Jan 2017 15:29:04: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:29:04: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:29:04: #1  total tags in treatment: 8805416 
INFO  @ Fri, 06 Jan 2017 15:29:04: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:29:04: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:29:04: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:29:04: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:29:04: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:29:04: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:29:04: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:29:04: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:32:03: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:35:10: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:35:17: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:35:23: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:35:29: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24331

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

Start	2017-01-06 15:35:47
End	2017-01-06 15:53:29
Elapsed	00:17:42
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_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--------------------
32762 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:36:09: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 150 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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 15:36:09: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:36:09: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:36:11:  1000000 
INFO  @ Fri, 06 Jan 2017 15:36:13:  2000000 
INFO  @ Fri, 06 Jan 2017 15:36:14:  3000000 
INFO  @ Fri, 06 Jan 2017 15:36:16:  4000000 
INFO  @ Fri, 06 Jan 2017 15:36:17:  5000000 
INFO  @ Fri, 06 Jan 2017 15:36:19:  6000000 
INFO  @ Fri, 06 Jan 2017 15:36:21:  7000000 
INFO  @ Fri, 06 Jan 2017 15:36:22:  8000000 
INFO  @ Fri, 06 Jan 2017 15:36:24: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:36:26:  1000000 
INFO  @ Fri, 06 Jan 2017 15:36:27:  2000000 
INFO  @ Fri, 06 Jan 2017 15:36:29:  3000000 
INFO  @ Fri, 06 Jan 2017 15:36:31:  4000000 
INFO  @ Fri, 06 Jan 2017 15:36:32:  5000000 
INFO  @ Fri, 06 Jan 2017 15:36:34:  6000000 
INFO  @ Fri, 06 Jan 2017 15:36:35:  7000000 
INFO  @ Fri, 06 Jan 2017 15:36:37:  8000000 
INFO  @ Fri, 06 Jan 2017 15:36:38:  9000000 
INFO  @ Fri, 06 Jan 2017 15:36:40:  10000000 
INFO  @ Fri, 06 Jan 2017 15:36:41:  11000000 
INFO  @ Fri, 06 Jan 2017 15:36:43:  12000000 
INFO  @ Fri, 06 Jan 2017 15:36:45:  13000000 
INFO  @ Fri, 06 Jan 2017 15:36:46:  14000000 
INFO  @ Fri, 06 Jan 2017 15:36:48:  15000000 
INFO  @ Fri, 06 Jan 2017 15:36:49:  16000000 
INFO  @ Fri, 06 Jan 2017 15:36:51:  17000000 
INFO  @ Fri, 06 Jan 2017 15:36:52:  18000000 
INFO  @ Fri, 06 Jan 2017 15:36:54:  19000000 
INFO  @ Fri, 06 Jan 2017 15:36:55:  20000000 
INFO  @ Fri, 06 Jan 2017 15:36:57:  21000000 
INFO  @ Fri, 06 Jan 2017 15:36:58:  22000000 
INFO  @ Fri, 06 Jan 2017 15:37:00:  23000000 
INFO  @ Fri, 06 Jan 2017 15:37:02:  24000000 
INFO  @ Fri, 06 Jan 2017 15:37:03:  25000000 
INFO  @ Fri, 06 Jan 2017 15:37:05:  26000000 
INFO  @ Fri, 06 Jan 2017 15:37:06:  27000000 
INFO  @ Fri, 06 Jan 2017 15:37:08:  28000000 
INFO  @ Fri, 06 Jan 2017 15:37:09:  29000000 
INFO  @ Fri, 06 Jan 2017 15:37:11:  30000000 
INFO  @ Fri, 06 Jan 2017 15:37:12:  31000000 
INFO  @ Fri, 06 Jan 2017 15:37:14:  32000000 
INFO  @ Fri, 06 Jan 2017 15:37:15:  33000000 
INFO  @ Fri, 06 Jan 2017 15:37:17:  34000000 
INFO  @ Fri, 06 Jan 2017 15:37:19:  35000000 
INFO  @ Fri, 06 Jan 2017 15:37:21:  36000000 
INFO  @ Fri, 06 Jan 2017 15:37:22:  37000000 
INFO  @ Fri, 06 Jan 2017 15:37:24:  38000000 
INFO  @ Fri, 06 Jan 2017 15:37:25:  39000000 
INFO  @ Fri, 06 Jan 2017 15:37:27:  40000000 
INFO  @ Fri, 06 Jan 2017 15:37:28:  41000000 
INFO  @ Fri, 06 Jan 2017 15:37:30:  42000000 
INFO  @ Fri, 06 Jan 2017 15:37:31:  43000000 
INFO  @ Fri, 06 Jan 2017 15:37:33:  44000000 
INFO  @ Fri, 06 Jan 2017 15:37:34:  45000000 
INFO  @ Fri, 06 Jan 2017 15:37:36:  46000000 
INFO  @ Fri, 06 Jan 2017 15:37:38:  47000000 
INFO  @ Fri, 06 Jan 2017 15:37:39:  48000000 
INFO  @ Fri, 06 Jan 2017 15:37:41:  49000000 
INFO  @ Fri, 06 Jan 2017 15:37:42:  50000000 
INFO  @ Fri, 06 Jan 2017 15:37:44: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:37:44: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:37:44: #1  total tags in treatment: 8805415 
INFO  @ Fri, 06 Jan 2017 15:37:44: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:37:44: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:37:44: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:37:44: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:37:44: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:37:44: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:37:44: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:37:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:41:01: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:41:01: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:41:01: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:41:01: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:41:01: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:46:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:46:09: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:46:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:46:10: Done! 
INFO  @ Fri, 06 Jan 2017 15:46:13: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 150 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/pseudo_reps/rep1/pr2/SRR1370896_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 15:46:13: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:46:13: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:46:15:  1000000 
INFO  @ Fri, 06 Jan 2017 15:46:16:  2000000 
INFO  @ Fri, 06 Jan 2017 15:46:18:  3000000 
INFO  @ Fri, 06 Jan 2017 15:46:20:  4000000 
INFO  @ Fri, 06 Jan 2017 15:46:21:  5000000 
INFO  @ Fri, 06 Jan 2017 15:46:23:  6000000 
INFO  @ Fri, 06 Jan 2017 15:46:24:  7000000 
INFO  @ Fri, 06 Jan 2017 15:46:26:  8000000 
INFO  @ Fri, 06 Jan 2017 15:46:28: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:46:29:  1000000 
INFO  @ Fri, 06 Jan 2017 15:46:31:  2000000 
INFO  @ Fri, 06 Jan 2017 15:46:32:  3000000 
INFO  @ Fri, 06 Jan 2017 15:46:34:  4000000 
INFO  @ Fri, 06 Jan 2017 15:46:35:  5000000 
INFO  @ Fri, 06 Jan 2017 15:46:37:  6000000 
INFO  @ Fri, 06 Jan 2017 15:46:38:  7000000 
INFO  @ Fri, 06 Jan 2017 15:46:40:  8000000 
INFO  @ Fri, 06 Jan 2017 15:46:41:  9000000 
INFO  @ Fri, 06 Jan 2017 15:46:43:  10000000 
INFO  @ Fri, 06 Jan 2017 15:46:44:  11000000 
INFO  @ Fri, 06 Jan 2017 15:46:46:  12000000 
INFO  @ Fri, 06 Jan 2017 15:46:47:  13000000 
INFO  @ Fri, 06 Jan 2017 15:46:49:  14000000 
INFO  @ Fri, 06 Jan 2017 15:46:50:  15000000 
INFO  @ Fri, 06 Jan 2017 15:46:52:  16000000 
INFO  @ Fri, 06 Jan 2017 15:46:53:  17000000 
INFO  @ Fri, 06 Jan 2017 15:46:54:  18000000 
INFO  @ Fri, 06 Jan 2017 15:46:56:  19000000 
INFO  @ Fri, 06 Jan 2017 15:46:57:  20000000 
INFO  @ Fri, 06 Jan 2017 15:46:59:  21000000 
INFO  @ Fri, 06 Jan 2017 15:47:00:  22000000 
INFO  @ Fri, 06 Jan 2017 15:47:02:  23000000 
INFO  @ Fri, 06 Jan 2017 15:47:03:  24000000 
INFO  @ Fri, 06 Jan 2017 15:47:05:  25000000 
INFO  @ Fri, 06 Jan 2017 15:47:06:  26000000 
INFO  @ Fri, 06 Jan 2017 15:47:08:  27000000 
INFO  @ Fri, 06 Jan 2017 15:47:09:  28000000 
INFO  @ Fri, 06 Jan 2017 15:47:11:  29000000 
INFO  @ Fri, 06 Jan 2017 15:47:12:  30000000 
INFO  @ Fri, 06 Jan 2017 15:47:14:  31000000 
INFO  @ Fri, 06 Jan 2017 15:47:15:  32000000 
INFO  @ Fri, 06 Jan 2017 15:47:17:  33000000 
INFO  @ Fri, 06 Jan 2017 15:47:18:  34000000 
INFO  @ Fri, 06 Jan 2017 15:47:20:  35000000 
INFO  @ Fri, 06 Jan 2017 15:47:21:  36000000 
INFO  @ Fri, 06 Jan 2017 15:47:23:  37000000 
INFO  @ Fri, 06 Jan 2017 15:47:24:  38000000 
INFO  @ Fri, 06 Jan 2017 15:47:26:  39000000 
INFO  @ Fri, 06 Jan 2017 15:47:27:  40000000 
INFO  @ Fri, 06 Jan 2017 15:47:29:  41000000 
INFO  @ Fri, 06 Jan 2017 15:47:30:  42000000 
INFO  @ Fri, 06 Jan 2017 15:47:32:  43000000 
INFO  @ Fri, 06 Jan 2017 15:47:33:  44000000 
INFO  @ Fri, 06 Jan 2017 15:47:35:  45000000 
INFO  @ Fri, 06 Jan 2017 15:47:36:  46000000 
INFO  @ Fri, 06 Jan 2017 15:47:38:  47000000 
INFO  @ Fri, 06 Jan 2017 15:47:39:  48000000 
INFO  @ Fri, 06 Jan 2017 15:47:40:  49000000 
INFO  @ Fri, 06 Jan 2017 15:47:42:  50000000 
INFO  @ Fri, 06 Jan 2017 15:47:44: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:47:44: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:47:44: #1  total tags in treatment: 8805415 
INFO  @ Fri, 06 Jan 2017 15:47:44: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:47:44: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:47:44: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:47:44: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:47:44: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:47:44: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:47:44: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:47:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:50:23: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:52:58: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:53:04: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:53:09: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:53:13: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24387

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

Start	2017-01-07 12:56:37
End	2017-01-07 12:57:53
Elapsed	00:01:16
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_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--------------------
36329 (process ID) old priority 0, new priority 10
Waiting for 56 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	168753	169023	.	0	.	15.2196396381056	-1	3.13192504997534	135

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270733.1	168753	169023	.	0	.	15.2196396381056	-1	3.13192504997534	135

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196483.1	11504	11780	.	0	.	13.7278702175475	-1	3.44142279815339	138

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KN196483.1	11504	11780	.	0	.	13.7278702175475	-1	3.44142279815339	138

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000205.2	1048	1318	.	0	.	3.24163522405746	-1	0.811111246256436	135

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000205.2	1048	1318	.	0	.	3.24163522405746	-1	0.811111246256436	135

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24388

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

Start	2017-01-07 12:57:54
End	2017-01-07 12:59:08
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370896_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370896_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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--------------------
36437 (process ID) old priority 0, new priority 10
Waiting for 17 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [0.99 1.19 0.74 0.23]
Number of reported peaks - 28099/28099 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 1449/28099 (5.2%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24389

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

Start	2017-01-07 12:59:09
End	2017-01-07 13:00:23
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/qc/ZSCAN31_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/ZSCAN31/out/qc/ZSCAN31_IDR_final.qc

# SYS command. line 224

 echo -e "0\t27	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/qc/ZSCAN31_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--------------------
36586 (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	53033

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

Start	2017-01-07 13:00:25
End	2017-01-07 13:01:33
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_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/ZSCAN31/out/peak/spp/rep1/SRR1370896_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--------------------
53037 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196483.1	11507	11777	.	0	.	22.5787461209494	-1	3.50219944265838	135

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/rep1/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KN196483.1	11507	11777	.	0	.	22.5787461209494	-1	3.50219944265838	135

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	57210

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

Start	2017-01-07 13:01:34
End	2017-01-07 13:01:43
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/spp/overlap/SRR1370896_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/ZSCAN31/out/peak/spp/overlap/SRR1370896_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
57214 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	932

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

Start	2017-01-07 13:01:44
End	2017-01-07 13:01:52
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_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/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/peak/idr/pseudo_reps/rep1/ZSCAN31_rep1-pr.IDR0.05.filt.12-col.bed.tmp

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

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	1471

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

Start	2017-01-07 13:01:53
End	2017-01-07 13:02:01
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/ZSCAN31/out/report/ZSCAN31_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/report/ZSCAN31_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/report/ZSCAN31_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
1475 (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, ZSCAN31, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZSCAN31/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZSCAN31/out/align/rep1/SRR1370896_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/ZSCAN31
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/ZSCAN31
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	34566.ZSCAN31.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