Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_143758_699
Start time	2017-01-06 14:37:58
Run time	1 day 02:33:16.848
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF35, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF35/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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_143758_699/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_143758_699/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_143758_699/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_143758_699/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_143758_699/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_143758_699/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_143758_699/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_143758_699/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_143758_699/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_143758_699/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_143758_699/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_143758_699/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_143758_699/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	24275

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

Start	2017-01-06 14:38:05
End	2017-01-07 17:05:49
Elapsed	1 day 02:27:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_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--------------------
36771 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz 
opened /tmp/24275.1.amd.q/Rtmpdva2Dj/SRR1370884_1.nodup.tagAlign90ee5afd2987
done. read 14432269 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24275.1.amd.q/Rtmpdva2Dj/input15MReadsNSCLess1.05.50MSubsample.tagAlign90ee6644b9b7
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1692027 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.197119701886758 
Top 3 estimates for fragment length 150 
Window half size 175 
Phantom peak location 55 
Phantom peak Correlation 0.1746582 
Normalized Strand cross-correlation coefficient (NSC) 1.164992 
Relative Strand cross-correlation Coefficient (RSC) 5.117252 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 3.509505  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.2849404  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000009 
Detected 566619 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/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2480	2656	.	0	.	23.3474370536557	-1	3.72973159528703	88

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2480	2656	.	0	.	23.3474370536557	-1	3.72973159528703	88

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24276

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

Start	2017-01-06 14:38:06
End	2017-01-06 17:53:31
Elapsed	03:15:25
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/signal/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/signal/macs2/rep1/SRR1370884_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/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1 -o "SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/signal/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1 -o "SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/signal/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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--------------------
36769 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:38:30: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 14:38:30: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:38:30: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:38:38:  1000000 
INFO  @ Fri, 06 Jan 2017 14:38:45:  2000000 
INFO  @ Fri, 06 Jan 2017 14:38:53:  3000000 
INFO  @ Fri, 06 Jan 2017 14:39:00:  4000000 
INFO  @ Fri, 06 Jan 2017 14:39:07:  5000000 
INFO  @ Fri, 06 Jan 2017 14:39:15:  6000000 
INFO  @ Fri, 06 Jan 2017 14:39:22:  7000000 
INFO  @ Fri, 06 Jan 2017 14:39:30:  8000000 
INFO  @ Fri, 06 Jan 2017 14:39:37:  9000000 
INFO  @ Fri, 06 Jan 2017 14:39:45:  10000000 
INFO  @ Fri, 06 Jan 2017 14:39:52:  11000000 
INFO  @ Fri, 06 Jan 2017 14:39:59:  12000000 
INFO  @ Fri, 06 Jan 2017 14:40:07:  13000000 
INFO  @ Fri, 06 Jan 2017 14:40:14:  14000000 
INFO  @ Fri, 06 Jan 2017 14:40:18: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:40:24:  1000000 
INFO  @ Fri, 06 Jan 2017 14:40:32:  2000000 
INFO  @ Fri, 06 Jan 2017 14:40:39:  3000000 
INFO  @ Fri, 06 Jan 2017 14:40:47:  4000000 
INFO  @ Fri, 06 Jan 2017 14:40:54:  5000000 
INFO  @ Fri, 06 Jan 2017 14:41:02:  6000000 
INFO  @ Fri, 06 Jan 2017 14:41:09:  7000000 
INFO  @ Fri, 06 Jan 2017 14:41:17:  8000000 
INFO  @ Fri, 06 Jan 2017 14:41:23:  9000000 
INFO  @ Fri, 06 Jan 2017 14:41:30:  10000000 
INFO  @ Fri, 06 Jan 2017 14:41:37:  11000000 
INFO  @ Fri, 06 Jan 2017 14:41:44:  12000000 
INFO  @ Fri, 06 Jan 2017 14:41:51:  13000000 
INFO  @ Fri, 06 Jan 2017 14:41:58:  14000000 
INFO  @ Fri, 06 Jan 2017 14:42:05:  15000000 
INFO  @ Fri, 06 Jan 2017 14:42:12:  16000000 
INFO  @ Fri, 06 Jan 2017 14:42:19:  17000000 
INFO  @ Fri, 06 Jan 2017 14:42:26:  18000000 
INFO  @ Fri, 06 Jan 2017 14:42:34:  19000000 
INFO  @ Fri, 06 Jan 2017 14:42:41:  20000000 
INFO  @ Fri, 06 Jan 2017 14:42:49:  21000000 
INFO  @ Fri, 06 Jan 2017 14:42:56:  22000000 
INFO  @ Fri, 06 Jan 2017 14:43:04:  23000000 
INFO  @ Fri, 06 Jan 2017 14:43:11:  24000000 
INFO  @ Fri, 06 Jan 2017 14:43:19:  25000000 
INFO  @ Fri, 06 Jan 2017 14:43:26:  26000000 
INFO  @ Fri, 06 Jan 2017 14:43:34:  27000000 
INFO  @ Fri, 06 Jan 2017 14:43:42:  28000000 
INFO  @ Fri, 06 Jan 2017 14:43:49:  29000000 
INFO  @ Fri, 06 Jan 2017 14:43:57:  30000000 
INFO  @ Fri, 06 Jan 2017 14:44:05:  31000000 
INFO  @ Fri, 06 Jan 2017 14:44:13:  32000000 
INFO  @ Fri, 06 Jan 2017 14:44:21:  33000000 
INFO  @ Fri, 06 Jan 2017 14:44:28:  34000000 
INFO  @ Fri, 06 Jan 2017 14:44:36:  35000000 
INFO  @ Fri, 06 Jan 2017 14:44:44:  36000000 
INFO  @ Fri, 06 Jan 2017 14:44:51:  37000000 
INFO  @ Fri, 06 Jan 2017 14:44:59:  38000000 
INFO  @ Fri, 06 Jan 2017 14:45:07:  39000000 
INFO  @ Fri, 06 Jan 2017 14:45:15:  40000000 
INFO  @ Fri, 06 Jan 2017 14:45:22:  41000000 
INFO  @ Fri, 06 Jan 2017 14:45:30:  42000000 
INFO  @ Fri, 06 Jan 2017 14:45:37:  43000000 
INFO  @ Fri, 06 Jan 2017 14:45:46:  44000000 
INFO  @ Fri, 06 Jan 2017 14:45:54:  45000000 
INFO  @ Fri, 06 Jan 2017 14:46:02:  46000000 
INFO  @ Fri, 06 Jan 2017 14:46:10:  47000000 
INFO  @ Fri, 06 Jan 2017 14:46:19:  48000000 
INFO  @ Fri, 06 Jan 2017 14:46:27:  49000000 
INFO  @ Fri, 06 Jan 2017 14:46:36:  50000000 
INFO  @ Fri, 06 Jan 2017 14:46:40: #1 tag size is determined as 48 bps 
INFO  @ Fri, 06 Jan 2017 14:46:40: #1 tag size = 48 
INFO  @ Fri, 06 Jan 2017 14:46:40: #1  total tags in treatment: 14432269 
INFO  @ Fri, 06 Jan 2017 14:46:40: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:46:40: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:46:40: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:46:40: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:46:40: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:46:40: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:46:40: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:46:40: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:56:13: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:56:13: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:56:13: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:56:13: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:56:13: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:16:17: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:16:22: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:16:28: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:16:31: Done! 
INFO  @ Fri, 06 Jan 2017 15:16:39: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_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/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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 15:16:39: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:16:39: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:16:47:  1000000 
INFO  @ Fri, 06 Jan 2017 15:16:55:  2000000 
INFO  @ Fri, 06 Jan 2017 15:17:03:  3000000 
INFO  @ Fri, 06 Jan 2017 15:17:11:  4000000 
INFO  @ Fri, 06 Jan 2017 15:17:19:  5000000 
INFO  @ Fri, 06 Jan 2017 15:17:27:  6000000 
INFO  @ Fri, 06 Jan 2017 15:17:35:  7000000 
INFO  @ Fri, 06 Jan 2017 15:17:43:  8000000 
INFO  @ Fri, 06 Jan 2017 15:17:51:  9000000 
INFO  @ Fri, 06 Jan 2017 15:17:59:  10000000 
INFO  @ Fri, 06 Jan 2017 15:18:08:  11000000 
INFO  @ Fri, 06 Jan 2017 15:18:16:  12000000 
INFO  @ Fri, 06 Jan 2017 15:18:25:  13000000 
INFO  @ Fri, 06 Jan 2017 15:18:32:  14000000 
INFO  @ Fri, 06 Jan 2017 15:18:36: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:18:44:  1000000 
INFO  @ Fri, 06 Jan 2017 15:18:53:  2000000 
INFO  @ Fri, 06 Jan 2017 15:19:02:  3000000 
INFO  @ Fri, 06 Jan 2017 15:19:11:  4000000 
INFO  @ Fri, 06 Jan 2017 15:19:19:  5000000 
INFO  @ Fri, 06 Jan 2017 15:19:27:  6000000 
INFO  @ Fri, 06 Jan 2017 15:19:36:  7000000 
INFO  @ Fri, 06 Jan 2017 15:19:44:  8000000 
INFO  @ Fri, 06 Jan 2017 15:19:52:  9000000 
INFO  @ Fri, 06 Jan 2017 15:20:00:  10000000 
INFO  @ Fri, 06 Jan 2017 15:20:08:  11000000 
INFO  @ Fri, 06 Jan 2017 15:20:17:  12000000 
INFO  @ Fri, 06 Jan 2017 15:20:25:  13000000 
INFO  @ Fri, 06 Jan 2017 15:20:33:  14000000 
INFO  @ Fri, 06 Jan 2017 15:20:41:  15000000 
INFO  @ Fri, 06 Jan 2017 15:20:49:  16000000 
INFO  @ Fri, 06 Jan 2017 15:20:57:  17000000 
INFO  @ Fri, 06 Jan 2017 15:21:05:  18000000 
INFO  @ Fri, 06 Jan 2017 15:21:13:  19000000 
INFO  @ Fri, 06 Jan 2017 15:21:21:  20000000 
INFO  @ Fri, 06 Jan 2017 15:21:29:  21000000 
INFO  @ Fri, 06 Jan 2017 15:21:37:  22000000 
INFO  @ Fri, 06 Jan 2017 15:21:45:  23000000 
INFO  @ Fri, 06 Jan 2017 15:21:52:  24000000 
INFO  @ Fri, 06 Jan 2017 15:22:01:  25000000 
INFO  @ Fri, 06 Jan 2017 15:22:08:  26000000 
INFO  @ Fri, 06 Jan 2017 15:22:16:  27000000 
INFO  @ Fri, 06 Jan 2017 15:22:24:  28000000 
INFO  @ Fri, 06 Jan 2017 15:22:32:  29000000 
INFO  @ Fri, 06 Jan 2017 15:22:40:  30000000 
INFO  @ Fri, 06 Jan 2017 15:22:48:  31000000 
INFO  @ Fri, 06 Jan 2017 15:22:56:  32000000 
INFO  @ Fri, 06 Jan 2017 15:23:04:  33000000 
INFO  @ Fri, 06 Jan 2017 15:23:12:  34000000 
INFO  @ Fri, 06 Jan 2017 15:23:20:  35000000 
INFO  @ Fri, 06 Jan 2017 15:23:29:  36000000 
INFO  @ Fri, 06 Jan 2017 15:23:36:  37000000 
INFO  @ Fri, 06 Jan 2017 15:23:44:  38000000 
INFO  @ Fri, 06 Jan 2017 15:23:53:  39000000 
INFO  @ Fri, 06 Jan 2017 15:24:01:  40000000 
INFO  @ Fri, 06 Jan 2017 15:24:09:  41000000 
INFO  @ Fri, 06 Jan 2017 15:24:17:  42000000 
INFO  @ Fri, 06 Jan 2017 15:24:25:  43000000 
INFO  @ Fri, 06 Jan 2017 15:24:33:  44000000 
INFO  @ Fri, 06 Jan 2017 15:24:41:  45000000 
INFO  @ Fri, 06 Jan 2017 15:24:49:  46000000 
INFO  @ Fri, 06 Jan 2017 15:24:57:  47000000 
INFO  @ Fri, 06 Jan 2017 15:25:05:  48000000 
INFO  @ Fri, 06 Jan 2017 15:25:13:  49000000 
INFO  @ Fri, 06 Jan 2017 15:25:21:  50000000 
INFO  @ Fri, 06 Jan 2017 15:25:25: #1 tag size is determined as 48 bps 
INFO  @ Fri, 06 Jan 2017 15:25:25: #1 tag size = 48 
INFO  @ Fri, 06 Jan 2017 15:25:25: #1  total tags in treatment: 14432269 
INFO  @ Fri, 06 Jan 2017 15:25:25: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:25:25: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:25:25: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:25:25: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:25:25: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:25:25: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:25:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:25:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:34:51: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:43:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:44:17: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:44:33: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:44:46: Done! 
INFO  @ Fri, 06 Jan 2017 15:45:22: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:47:37: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:55:35: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:58:07: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:20:09: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:28:44: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:43:21: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:45:24: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:53:03: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:56:09: Values in your input bedGraph files will be multiplied by 14.432269 ... 
INFO  @ Fri, 06 Jan 2017 17:17:41: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:19:45: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:32:17: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/rep1/SRR1370884_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	24277

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

Start	2017-01-06 14:38:06
End	2017-01-07 15:15:20
Elapsed	1 day 00:37:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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--------------------
36775 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign.gz 
opened /tmp/24277.1.amd.q/RtmpO0AIPj/SRR1370884_1.nodup.pr1.tagAlign90ed56f77235
done. read 7216135 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24277.1.amd.q/RtmpO0AIPj/input15MReadsNSCLess1.05.50MSubsample.tagAlign90ed6e918e04
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.09332688 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.108667357327026 
Top 3 estimates for fragment length 150 
Window half size 180 
Phantom peak location 55 
Phantom peak Correlation 0.09638885 
Normalized Strand cross-correlation coefficient (NSC) 1.164374 
Relative Strand cross-correlation Coefficient (RSC) 5.009994 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 6.985142  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.143161  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000579 
Detected 200970 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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270713.1	21700	21880	.	0	.	9.55587199640301	-1	3.55810830163055	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270713.1	21700	21880	.	0	.	9.55587199640301	-1	3.55810830163055	90

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24278

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

Start	2017-01-06 14:38:07
End	2017-01-07 15:18:42
Elapsed	1 day 00:40:34
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2 -speak=150 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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--------------------
36772 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign.gz 
opened /tmp/24278.1.amd.q/RtmpYPpG8R/SRR1370884_1.nodup.pr2.tagAlign90d56b941357
done. read 7216134 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24278.1.amd.q/RtmpYPpG8R/input15MReadsNSCLess1.05.50MSubsample.tagAlign90d524e4d044
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.09300206 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.108217801667408 
Top 3 estimates for fragment length 150 
Window half size 180 
Phantom peak location 50 
Phantom peak Correlation 0.09605966 
Normalized Strand cross-correlation coefficient (NSC) 1.163606 
Relative Strand cross-correlation Coefficient (RSC) 4.976373 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 6.98415  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1431813  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000729 
Detected 201471 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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2479	2659	.	0	.	16.85924890962	-1	3.22016238379682	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2479	2659	.	0	.	16.85924890962	-1	3.22016238379682	90

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24279

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

Start	2017-01-06 14:38:09
End	2017-01-06 15:41:26
Elapsed	01:03:16
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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--------------------
36785 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:38:30: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 14:38:30: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:38:30: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:38:36:  1000000 
INFO  @ Fri, 06 Jan 2017 14:38:43:  2000000 
INFO  @ Fri, 06 Jan 2017 14:38:50:  3000000 
INFO  @ Fri, 06 Jan 2017 14:38:57:  4000000 
INFO  @ Fri, 06 Jan 2017 14:39:03:  5000000 
INFO  @ Fri, 06 Jan 2017 14:39:10:  6000000 
INFO  @ Fri, 06 Jan 2017 14:39:16:  7000000 
INFO  @ Fri, 06 Jan 2017 14:39:18: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:39:25:  1000000 
INFO  @ Fri, 06 Jan 2017 14:39:31:  2000000 
INFO  @ Fri, 06 Jan 2017 14:39:38:  3000000 
INFO  @ Fri, 06 Jan 2017 14:39:44:  4000000 
INFO  @ Fri, 06 Jan 2017 14:39:51:  5000000 
INFO  @ Fri, 06 Jan 2017 14:39:57:  6000000 
INFO  @ Fri, 06 Jan 2017 14:40:04:  7000000 
INFO  @ Fri, 06 Jan 2017 14:40:10:  8000000 
INFO  @ Fri, 06 Jan 2017 14:40:17:  9000000 
INFO  @ Fri, 06 Jan 2017 14:40:24:  10000000 
INFO  @ Fri, 06 Jan 2017 14:40:31:  11000000 
INFO  @ Fri, 06 Jan 2017 14:40:37:  12000000 
INFO  @ Fri, 06 Jan 2017 14:40:44:  13000000 
INFO  @ Fri, 06 Jan 2017 14:40:50:  14000000 
INFO  @ Fri, 06 Jan 2017 14:40:57:  15000000 
INFO  @ Fri, 06 Jan 2017 14:41:03:  16000000 
INFO  @ Fri, 06 Jan 2017 14:41:10:  17000000 
INFO  @ Fri, 06 Jan 2017 14:41:17:  18000000 
INFO  @ Fri, 06 Jan 2017 14:41:24:  19000000 
INFO  @ Fri, 06 Jan 2017 14:41:30:  20000000 
INFO  @ Fri, 06 Jan 2017 14:41:37:  21000000 
INFO  @ Fri, 06 Jan 2017 14:41:44:  22000000 
INFO  @ Fri, 06 Jan 2017 14:41:52:  23000000 
INFO  @ Fri, 06 Jan 2017 14:41:59:  24000000 
INFO  @ Fri, 06 Jan 2017 14:42:06:  25000000 
INFO  @ Fri, 06 Jan 2017 14:42:13:  26000000 
INFO  @ Fri, 06 Jan 2017 14:42:21:  27000000 
INFO  @ Fri, 06 Jan 2017 14:42:28:  28000000 
INFO  @ Fri, 06 Jan 2017 14:42:35:  29000000 
INFO  @ Fri, 06 Jan 2017 14:42:42:  30000000 
INFO  @ Fri, 06 Jan 2017 14:42:49:  31000000 
INFO  @ Fri, 06 Jan 2017 14:42:57:  32000000 
INFO  @ Fri, 06 Jan 2017 14:43:04:  33000000 
INFO  @ Fri, 06 Jan 2017 14:43:12:  34000000 
INFO  @ Fri, 06 Jan 2017 14:43:19:  35000000 
INFO  @ Fri, 06 Jan 2017 14:43:27:  36000000 
INFO  @ Fri, 06 Jan 2017 14:43:35:  37000000 
INFO  @ Fri, 06 Jan 2017 14:43:43:  38000000 
INFO  @ Fri, 06 Jan 2017 14:43:50:  39000000 
INFO  @ Fri, 06 Jan 2017 14:43:58:  40000000 
INFO  @ Fri, 06 Jan 2017 14:44:06:  41000000 
INFO  @ Fri, 06 Jan 2017 14:44:13:  42000000 
INFO  @ Fri, 06 Jan 2017 14:44:21:  43000000 
INFO  @ Fri, 06 Jan 2017 14:44:29:  44000000 
INFO  @ Fri, 06 Jan 2017 14:44:37:  45000000 
INFO  @ Fri, 06 Jan 2017 14:44:45:  46000000 
INFO  @ Fri, 06 Jan 2017 14:44:52:  47000000 
INFO  @ Fri, 06 Jan 2017 14:45:00:  48000000 
INFO  @ Fri, 06 Jan 2017 14:45:08:  49000000 
INFO  @ Fri, 06 Jan 2017 14:45:16:  50000000 
INFO  @ Fri, 06 Jan 2017 14:45:20: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 14:45:20: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 14:45:20: #1  total tags in treatment: 7216135 
INFO  @ Fri, 06 Jan 2017 14:45:20: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:45:20: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:45:20: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:45:20: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:45:20: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:45:20: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:45:20: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:45:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:54:15: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:54:15: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:54:15: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:54:15: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:54:15: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:12:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:12:16: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:12:21: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:12:28: Done! 
INFO  @ Fri, 06 Jan 2017 15:12:36: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr1/SRR1370884_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 15:12:36: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:12:36: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:12:45:  1000000 
INFO  @ Fri, 06 Jan 2017 15:12:54:  2000000 
INFO  @ Fri, 06 Jan 2017 15:13:02:  3000000 
INFO  @ Fri, 06 Jan 2017 15:13:11:  4000000 
INFO  @ Fri, 06 Jan 2017 15:13:18:  5000000 
INFO  @ Fri, 06 Jan 2017 15:13:27:  6000000 
INFO  @ Fri, 06 Jan 2017 15:13:34:  7000000 
INFO  @ Fri, 06 Jan 2017 15:13:37: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:13:45:  1000000 
INFO  @ Fri, 06 Jan 2017 15:13:53:  2000000 
INFO  @ Fri, 06 Jan 2017 15:14:02:  3000000 
INFO  @ Fri, 06 Jan 2017 15:14:10:  4000000 
INFO  @ Fri, 06 Jan 2017 15:14:17:  5000000 
INFO  @ Fri, 06 Jan 2017 15:14:25:  6000000 
INFO  @ Fri, 06 Jan 2017 15:14:33:  7000000 
INFO  @ Fri, 06 Jan 2017 15:14:42:  8000000 
INFO  @ Fri, 06 Jan 2017 15:14:50:  9000000 
INFO  @ Fri, 06 Jan 2017 15:14:58:  10000000 
INFO  @ Fri, 06 Jan 2017 15:15:05:  11000000 
INFO  @ Fri, 06 Jan 2017 15:15:13:  12000000 
INFO  @ Fri, 06 Jan 2017 15:15:21:  13000000 
INFO  @ Fri, 06 Jan 2017 15:15:29:  14000000 
INFO  @ Fri, 06 Jan 2017 15:15:37:  15000000 
INFO  @ Fri, 06 Jan 2017 15:15:44:  16000000 
INFO  @ Fri, 06 Jan 2017 15:15:52:  17000000 
INFO  @ Fri, 06 Jan 2017 15:16:00:  18000000 
INFO  @ Fri, 06 Jan 2017 15:16:08:  19000000 
INFO  @ Fri, 06 Jan 2017 15:16:16:  20000000 
INFO  @ Fri, 06 Jan 2017 15:16:24:  21000000 
INFO  @ Fri, 06 Jan 2017 15:16:32:  22000000 
INFO  @ Fri, 06 Jan 2017 15:16:40:  23000000 
INFO  @ Fri, 06 Jan 2017 15:16:48:  24000000 
INFO  @ Fri, 06 Jan 2017 15:16:55:  25000000 
INFO  @ Fri, 06 Jan 2017 15:17:03:  26000000 
INFO  @ Fri, 06 Jan 2017 15:17:11:  27000000 
INFO  @ Fri, 06 Jan 2017 15:17:19:  28000000 
INFO  @ Fri, 06 Jan 2017 15:17:27:  29000000 
INFO  @ Fri, 06 Jan 2017 15:17:35:  30000000 
INFO  @ Fri, 06 Jan 2017 15:17:44:  31000000 
INFO  @ Fri, 06 Jan 2017 15:17:52:  32000000 
INFO  @ Fri, 06 Jan 2017 15:17:59:  33000000 
INFO  @ Fri, 06 Jan 2017 15:18:07:  34000000 
INFO  @ Fri, 06 Jan 2017 15:18:15:  35000000 
INFO  @ Fri, 06 Jan 2017 15:18:24:  36000000 
INFO  @ Fri, 06 Jan 2017 15:18:32:  37000000 
INFO  @ Fri, 06 Jan 2017 15:18:40:  38000000 
INFO  @ Fri, 06 Jan 2017 15:18:49:  39000000 
INFO  @ Fri, 06 Jan 2017 15:18:56:  40000000 
INFO  @ Fri, 06 Jan 2017 15:19:03:  41000000 
INFO  @ Fri, 06 Jan 2017 15:19:10:  42000000 
INFO  @ Fri, 06 Jan 2017 15:19:18:  43000000 
INFO  @ Fri, 06 Jan 2017 15:19:25:  44000000 
INFO  @ Fri, 06 Jan 2017 15:19:33:  45000000 
INFO  @ Fri, 06 Jan 2017 15:19:42:  46000000 
INFO  @ Fri, 06 Jan 2017 15:19:50:  47000000 
INFO  @ Fri, 06 Jan 2017 15:19:59:  48000000 
INFO  @ Fri, 06 Jan 2017 15:20:07:  49000000 
INFO  @ Fri, 06 Jan 2017 15:20:14:  50000000 
INFO  @ Fri, 06 Jan 2017 15:20:18: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:20:18: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:20:18: #1  total tags in treatment: 7216135 
INFO  @ Fri, 06 Jan 2017 15:20:18: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:20:18: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:20:18: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:20:18: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:20:18: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:20:18: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:20:18: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:20:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:28:58: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:39:29: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:40:00: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:40:26: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:40:44: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24335

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

Start	2017-01-06 15:41:28
End	2017-01-06 16:40:23
Elapsed	00:58:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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--------------------
42599 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:42:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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 15:42:02: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:42:02: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:42:09:  1000000 
INFO  @ Fri, 06 Jan 2017 15:42:17:  2000000 
INFO  @ Fri, 06 Jan 2017 15:42:24:  3000000 
INFO  @ Fri, 06 Jan 2017 15:42:32:  4000000 
INFO  @ Fri, 06 Jan 2017 15:42:41:  5000000 
INFO  @ Fri, 06 Jan 2017 15:42:48:  6000000 
INFO  @ Fri, 06 Jan 2017 15:42:56:  7000000 
INFO  @ Fri, 06 Jan 2017 15:42:59: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:43:06:  1000000 
INFO  @ Fri, 06 Jan 2017 15:43:14:  2000000 
INFO  @ Fri, 06 Jan 2017 15:43:21:  3000000 
INFO  @ Fri, 06 Jan 2017 15:43:29:  4000000 
INFO  @ Fri, 06 Jan 2017 15:43:36:  5000000 
INFO  @ Fri, 06 Jan 2017 15:43:44:  6000000 
INFO  @ Fri, 06 Jan 2017 15:43:51:  7000000 
INFO  @ Fri, 06 Jan 2017 15:43:59:  8000000 
INFO  @ Fri, 06 Jan 2017 15:44:06:  9000000 
INFO  @ Fri, 06 Jan 2017 15:44:14:  10000000 
INFO  @ Fri, 06 Jan 2017 15:44:21:  11000000 
INFO  @ Fri, 06 Jan 2017 15:44:28:  12000000 
INFO  @ Fri, 06 Jan 2017 15:44:36:  13000000 
INFO  @ Fri, 06 Jan 2017 15:44:43:  14000000 
INFO  @ Fri, 06 Jan 2017 15:44:51:  15000000 
INFO  @ Fri, 06 Jan 2017 15:44:59:  16000000 
INFO  @ Fri, 06 Jan 2017 15:45:07:  17000000 
INFO  @ Fri, 06 Jan 2017 15:45:14:  18000000 
INFO  @ Fri, 06 Jan 2017 15:45:22:  19000000 
INFO  @ Fri, 06 Jan 2017 15:45:29:  20000000 
INFO  @ Fri, 06 Jan 2017 15:45:36:  21000000 
INFO  @ Fri, 06 Jan 2017 15:45:44:  22000000 
INFO  @ Fri, 06 Jan 2017 15:45:51:  23000000 
INFO  @ Fri, 06 Jan 2017 15:45:59:  24000000 
INFO  @ Fri, 06 Jan 2017 15:46:06:  25000000 
INFO  @ Fri, 06 Jan 2017 15:46:14:  26000000 
INFO  @ Fri, 06 Jan 2017 15:46:21:  27000000 
INFO  @ Fri, 06 Jan 2017 15:46:29:  28000000 
INFO  @ Fri, 06 Jan 2017 15:46:36:  29000000 
INFO  @ Fri, 06 Jan 2017 15:46:44:  30000000 
INFO  @ Fri, 06 Jan 2017 15:46:52:  31000000 
INFO  @ Fri, 06 Jan 2017 15:46:59:  32000000 
INFO  @ Fri, 06 Jan 2017 15:47:06:  33000000 
INFO  @ Fri, 06 Jan 2017 15:47:14:  34000000 
INFO  @ Fri, 06 Jan 2017 15:47:21:  35000000 
INFO  @ Fri, 06 Jan 2017 15:47:29:  36000000 
INFO  @ Fri, 06 Jan 2017 15:47:36:  37000000 
INFO  @ Fri, 06 Jan 2017 15:47:43:  38000000 
INFO  @ Fri, 06 Jan 2017 15:47:50:  39000000 
INFO  @ Fri, 06 Jan 2017 15:47:57:  40000000 
INFO  @ Fri, 06 Jan 2017 15:48:05:  41000000 
INFO  @ Fri, 06 Jan 2017 15:48:12:  42000000 
INFO  @ Fri, 06 Jan 2017 15:48:20:  43000000 
INFO  @ Fri, 06 Jan 2017 15:48:27:  44000000 
INFO  @ Fri, 06 Jan 2017 15:48:34:  45000000 
INFO  @ Fri, 06 Jan 2017 15:48:42:  46000000 
INFO  @ Fri, 06 Jan 2017 15:48:49:  47000000 
INFO  @ Fri, 06 Jan 2017 15:48:57:  48000000 
INFO  @ Fri, 06 Jan 2017 15:49:04:  49000000 
INFO  @ Fri, 06 Jan 2017 15:49:12:  50000000 
INFO  @ Fri, 06 Jan 2017 15:49:15: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:49:15: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:49:15: #1  total tags in treatment: 7216134 
INFO  @ Fri, 06 Jan 2017 15:49:15: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:49:15: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:49:15: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:49:15: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:49:15: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:49:15: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:49:15: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:49:15: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:57:42: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:57:42: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:57:42: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:57:42: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:57:42: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:15:11: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:15:17: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 16:15:21: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 16:15:24: Done! 
INFO  @ Fri, 06 Jan 2017 16:15:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 16:15:32: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 16:15:32: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 16:15:40:  1000000 
INFO  @ Fri, 06 Jan 2017 16:15:47:  2000000 
INFO  @ Fri, 06 Jan 2017 16:15:54:  3000000 
INFO  @ Fri, 06 Jan 2017 16:16:01:  4000000 
INFO  @ Fri, 06 Jan 2017 16:16:08:  5000000 
INFO  @ Fri, 06 Jan 2017 16:16:16:  6000000 
INFO  @ Fri, 06 Jan 2017 16:16:23:  7000000 
INFO  @ Fri, 06 Jan 2017 16:16:25: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 16:16:32:  1000000 
INFO  @ Fri, 06 Jan 2017 16:16:39:  2000000 
INFO  @ Fri, 06 Jan 2017 16:16:46:  3000000 
INFO  @ Fri, 06 Jan 2017 16:16:53:  4000000 
INFO  @ Fri, 06 Jan 2017 16:17:00:  5000000 
INFO  @ Fri, 06 Jan 2017 16:17:07:  6000000 
INFO  @ Fri, 06 Jan 2017 16:17:14:  7000000 
INFO  @ Fri, 06 Jan 2017 16:17:21:  8000000 
INFO  @ Fri, 06 Jan 2017 16:17:28:  9000000 
INFO  @ Fri, 06 Jan 2017 16:17:35:  10000000 
INFO  @ Fri, 06 Jan 2017 16:17:42:  11000000 
INFO  @ Fri, 06 Jan 2017 16:17:50:  12000000 
INFO  @ Fri, 06 Jan 2017 16:17:57:  13000000 
INFO  @ Fri, 06 Jan 2017 16:18:04:  14000000 
INFO  @ Fri, 06 Jan 2017 16:18:11:  15000000 
INFO  @ Fri, 06 Jan 2017 16:18:18:  16000000 
INFO  @ Fri, 06 Jan 2017 16:18:25:  17000000 
INFO  @ Fri, 06 Jan 2017 16:18:32:  18000000 
INFO  @ Fri, 06 Jan 2017 16:18:39:  19000000 
INFO  @ Fri, 06 Jan 2017 16:18:46:  20000000 
INFO  @ Fri, 06 Jan 2017 16:18:53:  21000000 
INFO  @ Fri, 06 Jan 2017 16:19:00:  22000000 
INFO  @ Fri, 06 Jan 2017 16:19:07:  23000000 
INFO  @ Fri, 06 Jan 2017 16:19:14:  24000000 
INFO  @ Fri, 06 Jan 2017 16:19:22:  25000000 
INFO  @ Fri, 06 Jan 2017 16:19:29:  26000000 
INFO  @ Fri, 06 Jan 2017 16:19:36:  27000000 
INFO  @ Fri, 06 Jan 2017 16:19:43:  28000000 
INFO  @ Fri, 06 Jan 2017 16:19:50:  29000000 
INFO  @ Fri, 06 Jan 2017 16:19:57:  30000000 
INFO  @ Fri, 06 Jan 2017 16:20:04:  31000000 
INFO  @ Fri, 06 Jan 2017 16:20:11:  32000000 
INFO  @ Fri, 06 Jan 2017 16:20:18:  33000000 
INFO  @ Fri, 06 Jan 2017 16:20:25:  34000000 
INFO  @ Fri, 06 Jan 2017 16:20:32:  35000000 
INFO  @ Fri, 06 Jan 2017 16:20:39:  36000000 
INFO  @ Fri, 06 Jan 2017 16:20:46:  37000000 
INFO  @ Fri, 06 Jan 2017 16:20:53:  38000000 
INFO  @ Fri, 06 Jan 2017 16:21:01:  39000000 
INFO  @ Fri, 06 Jan 2017 16:21:08:  40000000 
INFO  @ Fri, 06 Jan 2017 16:21:15:  41000000 
INFO  @ Fri, 06 Jan 2017 16:21:22:  42000000 
INFO  @ Fri, 06 Jan 2017 16:21:29:  43000000 
INFO  @ Fri, 06 Jan 2017 16:21:36:  44000000 
INFO  @ Fri, 06 Jan 2017 16:21:44:  45000000 
INFO  @ Fri, 06 Jan 2017 16:21:51:  46000000 
INFO  @ Fri, 06 Jan 2017 16:21:59:  47000000 
INFO  @ Fri, 06 Jan 2017 16:22:06:  48000000 
INFO  @ Fri, 06 Jan 2017 16:22:14:  49000000 
INFO  @ Fri, 06 Jan 2017 16:22:21:  50000000 
INFO  @ Fri, 06 Jan 2017 16:22:25: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 16:22:25: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 16:22:25: #1  total tags in treatment: 7216134 
INFO  @ Fri, 06 Jan 2017 16:22:25: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 16:22:25: #1 finished! 
INFO  @ Fri, 06 Jan 2017 16:22:25: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 16:22:25: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 16:22:25: #2 Use 150 as fragment length 
INFO  @ Fri, 06 Jan 2017 16:22:25: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 16:22:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 16:22:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:29:53: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:38:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:39:10: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:39:30: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:39:46: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24394

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

Start	2017-01-07 17:05:51
End	2017-01-07 17:07:08
Elapsed	00:01:17
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_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--------------------
41219 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270713.1	21700	21880	.	0	.	9.55587199640301	-1	3.55810830163055	90

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270713.1	21700	21880	.	0	.	9.55587199640301	-1	3.55810830163055	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2479	2659	.	0	.	16.85924890962	-1	3.22016238379682	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2479	2659	.	0	.	16.85924890962	-1	3.22016238379682	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	68705	68881	.	0	.	5.0083268423062	-1	3.31172478249856	88

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL000195.1	68705	68881	.	0	.	5.0083268423062	-1	3.31172478249856	88

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24395

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

Start	2017-01-07 17:07:10
End	2017-01-07 17:08:21
Elapsed	00:01:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370884_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370884_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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--------------------
41322 (process ID) old priority 0, new priority 10
Waiting for 12 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.00 1.17 0.74 0.36]
Number of reported peaks - 28929/28929 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 2869/28929 (9.9%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24396

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

Start	2017-01-07 17:08:22
End	2017-01-07 17:09:37
Elapsed	00:01:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/qc/ZNF35_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/ZNF35/out/qc/ZNF35_IDR_final.qc

# SYS command. line 224

 echo -e "0\t64	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/qc/ZNF35_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--------------------
41468 (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	21393

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

Start	2017-01-07 17:09:39
End	2017-01-07 17:10:47
Elapsed	00:01:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_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/ZNF35/out/peak/spp/rep1/SRR1370884_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--------------------
21397 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2480	2656	.	0	.	23.3474370536557	-1	3.72973159528703	88

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/rep1/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2480	2656	.	0	.	23.3474370536557	-1	3.72973159528703	88

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	25353

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

Start	2017-01-07 17:10:48
End	2017-01-07 17:10:56
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/spp/overlap/SRR1370884_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/ZNF35/out/peak/spp/overlap/SRR1370884_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
25357 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	25937

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

Start	2017-01-07 17:10:57
End	2017-01-07 17:11:06
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_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/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/peak/idr/pseudo_reps/rep1/ZNF35_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
25941 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	26502

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

Start	2017-01-07 17:11:07
End	2017-01-07 17:11:15
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/ZNF35/out/report/ZNF35_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/report/ZNF35_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/report/ZNF35_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
26506 (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, ZNF35, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF35/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF35/out/align/rep1/SRR1370884_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/ZNF35
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/ZNF35
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	1652.ZNF35.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