Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_144429_675
Start time	2017-01-06 14:44:29
Run time	1 day 10:50:46.839
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF574, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF574/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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_144429_675/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_144429_675/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_144429_675/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_144429_675/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_144429_675/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_144429_675/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_144429_675/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_144429_675/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_144429_675/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_144429_675/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_144429_675/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_144429_675/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_144429_675/task.graphviz.report.line_97.id_24
thread_41	thread_Root
thread_42	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	24299

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

Start	2017-01-06 14:44:34
End	2017-01-07 10:06:37
Elapsed	19:22:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_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--------------------
30434 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_1.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/align/rep1/SRR1370897_1.nodup.tagAlign.gz 
opened /tmp/24299.1.q/RtmpajkbRR/SRR1370897_1.nodup.tagAlign77221fa0ba49
done. read 16824589 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/24299.1.q/RtmpajkbRR/input15MReadsNSCLess1.05.50MSubsample.tagAlign77222f68e437
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.189438 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.22459468898376 
Top 3 estimates for fragment length 145 
Window half size 245 
Phantom peak location 55 
Phantom peak Correlation 0.2046668 
Normalized Strand cross-correlation coefficient (NSC) 1.185584 
Relative Strand cross-correlation Coefficient (RSC) 2.308561 
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= 3.036009  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.3293798  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000038 
Detected 587230 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/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3203	3447	.	0	.	35.5338705952906	-1	3.85871761486029	122

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3203	3447	.	0	.	35.5338705952906	-1	3.85871761486029	122

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24300

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

Start	2017-01-06 14:44:35
End	2017-01-06 18:04:07
Elapsed	03:19:31
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/signal/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/signal/macs2/rep1/SRR1370897_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/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1 -o "SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/signal/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1 -o "SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/signal/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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--------------------
39418 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:45:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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 14:45:01: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:45:01: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:45:09:  1000000 
INFO  @ Fri, 06 Jan 2017 14:45:16:  2000000 
INFO  @ Fri, 06 Jan 2017 14:45:24:  3000000 
INFO  @ Fri, 06 Jan 2017 14:45:32:  4000000 
INFO  @ Fri, 06 Jan 2017 14:45:40:  5000000 
INFO  @ Fri, 06 Jan 2017 14:45:48:  6000000 
INFO  @ Fri, 06 Jan 2017 14:45:56:  7000000 
INFO  @ Fri, 06 Jan 2017 14:46:04:  8000000 
INFO  @ Fri, 06 Jan 2017 14:46:13:  9000000 
INFO  @ Fri, 06 Jan 2017 14:46:21:  10000000 
INFO  @ Fri, 06 Jan 2017 14:46:30:  11000000 
INFO  @ Fri, 06 Jan 2017 14:46:38:  12000000 
INFO  @ Fri, 06 Jan 2017 14:46:46:  13000000 
INFO  @ Fri, 06 Jan 2017 14:46:54:  14000000 
INFO  @ Fri, 06 Jan 2017 14:47:01:  15000000 
INFO  @ Fri, 06 Jan 2017 14:47:08:  16000000 
INFO  @ Fri, 06 Jan 2017 14:47:15: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:47:23:  1000000 
INFO  @ Fri, 06 Jan 2017 14:47:30:  2000000 
INFO  @ Fri, 06 Jan 2017 14:47:38:  3000000 
INFO  @ Fri, 06 Jan 2017 14:47:46:  4000000 
INFO  @ Fri, 06 Jan 2017 14:47:53:  5000000 
INFO  @ Fri, 06 Jan 2017 14:48:01:  6000000 
INFO  @ Fri, 06 Jan 2017 14:48:09:  7000000 
INFO  @ Fri, 06 Jan 2017 14:48:17:  8000000 
INFO  @ Fri, 06 Jan 2017 14:48:25:  9000000 
INFO  @ Fri, 06 Jan 2017 14:48:34:  10000000 
INFO  @ Fri, 06 Jan 2017 14:48:42:  11000000 
INFO  @ Fri, 06 Jan 2017 14:48:50:  12000000 
INFO  @ Fri, 06 Jan 2017 14:48:57:  13000000 
INFO  @ Fri, 06 Jan 2017 14:49:05:  14000000 
INFO  @ Fri, 06 Jan 2017 14:49:12:  15000000 
INFO  @ Fri, 06 Jan 2017 14:49:21:  16000000 
INFO  @ Fri, 06 Jan 2017 14:49:29:  17000000 
INFO  @ Fri, 06 Jan 2017 14:49:37:  18000000 
INFO  @ Fri, 06 Jan 2017 14:49:46:  19000000 
INFO  @ Fri, 06 Jan 2017 14:49:54:  20000000 
INFO  @ Fri, 06 Jan 2017 14:50:03:  21000000 
INFO  @ Fri, 06 Jan 2017 14:50:11:  22000000 
INFO  @ Fri, 06 Jan 2017 14:50:20:  23000000 
INFO  @ Fri, 06 Jan 2017 14:50:28:  24000000 
INFO  @ Fri, 06 Jan 2017 14:50:36:  25000000 
INFO  @ Fri, 06 Jan 2017 14:50:45:  26000000 
INFO  @ Fri, 06 Jan 2017 14:50:53:  27000000 
INFO  @ Fri, 06 Jan 2017 14:51:01:  28000000 
INFO  @ Fri, 06 Jan 2017 14:51:10:  29000000 
INFO  @ Fri, 06 Jan 2017 14:51:18:  30000000 
INFO  @ Fri, 06 Jan 2017 14:51:26:  31000000 
INFO  @ Fri, 06 Jan 2017 14:51:35:  32000000 
INFO  @ Fri, 06 Jan 2017 14:51:43:  33000000 
INFO  @ Fri, 06 Jan 2017 14:51:52:  34000000 
INFO  @ Fri, 06 Jan 2017 14:52:00:  35000000 
INFO  @ Fri, 06 Jan 2017 14:52:08:  36000000 
INFO  @ Fri, 06 Jan 2017 14:52:16:  37000000 
INFO  @ Fri, 06 Jan 2017 14:52:25:  38000000 
INFO  @ Fri, 06 Jan 2017 14:52:32:  39000000 
INFO  @ Fri, 06 Jan 2017 14:52:39:  40000000 
INFO  @ Fri, 06 Jan 2017 14:52:48:  41000000 
INFO  @ Fri, 06 Jan 2017 14:52:55:  42000000 
INFO  @ Fri, 06 Jan 2017 14:53:03:  43000000 
INFO  @ Fri, 06 Jan 2017 14:53:12:  44000000 
INFO  @ Fri, 06 Jan 2017 14:53:20:  45000000 
INFO  @ Fri, 06 Jan 2017 14:53:30:  46000000 
INFO  @ Fri, 06 Jan 2017 14:53:39:  47000000 
INFO  @ Fri, 06 Jan 2017 14:53:48:  48000000 
INFO  @ Fri, 06 Jan 2017 14:53:57:  49000000 
INFO  @ Fri, 06 Jan 2017 14:54:05:  50000000 
INFO  @ Fri, 06 Jan 2017 14:54:09: #1 tag size is determined as 48 bps 
INFO  @ Fri, 06 Jan 2017 14:54:09: #1 tag size = 48 
INFO  @ Fri, 06 Jan 2017 14:54:09: #1  total tags in treatment: 16824589 
INFO  @ Fri, 06 Jan 2017 14:54:09: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:54:09: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:54:09: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:54:09: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:54:09: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:54:09: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:54:09: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:54:09: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:04:22: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:04:22: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:04:22: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:04:22: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:04:22: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:26:16: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:26:20: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:26:22: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:26:24: Done! 
INFO  @ Fri, 06 Jan 2017 15:26:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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 15:26:31: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:26:31: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:26:38:  1000000 
INFO  @ Fri, 06 Jan 2017 15:26:46:  2000000 
INFO  @ Fri, 06 Jan 2017 15:26:53:  3000000 
INFO  @ Fri, 06 Jan 2017 15:27:00:  4000000 
INFO  @ Fri, 06 Jan 2017 15:27:08:  5000000 
INFO  @ Fri, 06 Jan 2017 15:27:16:  6000000 
INFO  @ Fri, 06 Jan 2017 15:27:24:  7000000 
INFO  @ Fri, 06 Jan 2017 15:27:31:  8000000 
INFO  @ Fri, 06 Jan 2017 15:27:39:  9000000 
INFO  @ Fri, 06 Jan 2017 15:27:46:  10000000 
INFO  @ Fri, 06 Jan 2017 15:27:54:  11000000 
INFO  @ Fri, 06 Jan 2017 15:28:01:  12000000 
INFO  @ Fri, 06 Jan 2017 15:28:09:  13000000 
INFO  @ Fri, 06 Jan 2017 15:28:17:  14000000 
INFO  @ Fri, 06 Jan 2017 15:28:24:  15000000 
INFO  @ Fri, 06 Jan 2017 15:28:32:  16000000 
INFO  @ Fri, 06 Jan 2017 15:28:39: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:28:46:  1000000 
INFO  @ Fri, 06 Jan 2017 15:28:54:  2000000 
INFO  @ Fri, 06 Jan 2017 15:29:02:  3000000 
INFO  @ Fri, 06 Jan 2017 15:29:09:  4000000 
INFO  @ Fri, 06 Jan 2017 15:29:17:  5000000 
INFO  @ Fri, 06 Jan 2017 15:29:25:  6000000 
INFO  @ Fri, 06 Jan 2017 15:29:33:  7000000 
INFO  @ Fri, 06 Jan 2017 15:29:42:  8000000 
INFO  @ Fri, 06 Jan 2017 15:29:49:  9000000 
INFO  @ Fri, 06 Jan 2017 15:29:57:  10000000 
INFO  @ Fri, 06 Jan 2017 15:30:04:  11000000 
INFO  @ Fri, 06 Jan 2017 15:30:12:  12000000 
INFO  @ Fri, 06 Jan 2017 15:30:19:  13000000 
INFO  @ Fri, 06 Jan 2017 15:30:27:  14000000 
INFO  @ Fri, 06 Jan 2017 15:30:35:  15000000 
INFO  @ Fri, 06 Jan 2017 15:30:43:  16000000 
INFO  @ Fri, 06 Jan 2017 15:30:51:  17000000 
INFO  @ Fri, 06 Jan 2017 15:30:59:  18000000 
INFO  @ Fri, 06 Jan 2017 15:31:07:  19000000 
INFO  @ Fri, 06 Jan 2017 15:31:14:  20000000 
INFO  @ Fri, 06 Jan 2017 15:31:22:  21000000 
INFO  @ Fri, 06 Jan 2017 15:31:30:  22000000 
INFO  @ Fri, 06 Jan 2017 15:31:37:  23000000 
INFO  @ Fri, 06 Jan 2017 15:31:45:  24000000 
INFO  @ Fri, 06 Jan 2017 15:31:53:  25000000 
INFO  @ Fri, 06 Jan 2017 15:32:01:  26000000 
INFO  @ Fri, 06 Jan 2017 15:32:08:  27000000 
INFO  @ Fri, 06 Jan 2017 15:32:16:  28000000 
INFO  @ Fri, 06 Jan 2017 15:32:23:  29000000 
INFO  @ Fri, 06 Jan 2017 15:32:31:  30000000 
INFO  @ Fri, 06 Jan 2017 15:32:38:  31000000 
INFO  @ Fri, 06 Jan 2017 15:32:45:  32000000 
INFO  @ Fri, 06 Jan 2017 15:32:53:  33000000 
INFO  @ Fri, 06 Jan 2017 15:33:01:  34000000 
INFO  @ Fri, 06 Jan 2017 15:33:09:  35000000 
INFO  @ Fri, 06 Jan 2017 15:33:16:  36000000 
INFO  @ Fri, 06 Jan 2017 15:33:24:  37000000 
INFO  @ Fri, 06 Jan 2017 15:33:31:  38000000 
INFO  @ Fri, 06 Jan 2017 15:33:39:  39000000 
INFO  @ Fri, 06 Jan 2017 15:33:46:  40000000 
INFO  @ Fri, 06 Jan 2017 15:33:54:  41000000 
INFO  @ Fri, 06 Jan 2017 15:34:02:  42000000 
INFO  @ Fri, 06 Jan 2017 15:34:09:  43000000 
INFO  @ Fri, 06 Jan 2017 15:34:17:  44000000 
INFO  @ Fri, 06 Jan 2017 15:34:24:  45000000 
INFO  @ Fri, 06 Jan 2017 15:34:32:  46000000 
INFO  @ Fri, 06 Jan 2017 15:34:39:  47000000 
INFO  @ Fri, 06 Jan 2017 15:34:47:  48000000 
INFO  @ Fri, 06 Jan 2017 15:34:54:  49000000 
INFO  @ Fri, 06 Jan 2017 15:35:02:  50000000 
INFO  @ Fri, 06 Jan 2017 15:35:06: #1 tag size is determined as 48 bps 
INFO  @ Fri, 06 Jan 2017 15:35:06: #1 tag size = 48 
INFO  @ Fri, 06 Jan 2017 15:35:06: #1  total tags in treatment: 16824589 
INFO  @ Fri, 06 Jan 2017 15:35:06: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:35:06: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:35:06: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:35:06: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:35:06: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:35:06: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:35:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:35:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:44:02: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:52:31: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:52:53: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:53:10: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:53:23: Done! 
INFO  @ Fri, 06 Jan 2017 15:53:56: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:56:19: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:04:02: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 16:06:35: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 16:29:05: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 16:38:50: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 16:55:08: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 16:57:27: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 17:04:53: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 17:07:33: Values in your input bedGraph files will be multiplied by 16.824589 ... 
INFO  @ Fri, 06 Jan 2017 17:30:03: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 17:32:17: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 17:44:34: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/rep1/SRR1370897_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	24301

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

Start	2017-01-06 14:44:36
End	2017-01-08 01:25:41
Elapsed	1 day 10:41:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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--------------------
39427 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign.gz 
opened /tmp/24301.1.amd.q/RtmpNo0F0e/SRR1370897_1.nodup.pr1.tagAlign9b00dda46b1
done. read 8412295 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/24301.1.amd.q/RtmpNo0F0e/input15MReadsNSCLess1.05.50MSubsample.tagAlign9b003256a860
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1063917 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.12598700073388 
Top 3 estimates for fragment length 145 
Window half size 245 
Phantom peak location 55 
Phantom peak Correlation 0.1149522 
Normalized Strand cross-correlation coefficient (NSC) 1.184181 
Relative Strand cross-correlation Coefficient (RSC) 2.289045 
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= 6.047258  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1653642  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000124 
Detected 224274 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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3181	3425	.	0	.	23.2994651818338	-1	3.52207368618481	122

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3181	3425	.	0	.	23.2994651818338	-1	3.52207368618481	122

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24302

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

Start	2017-01-06 14:44:37
End	2017-01-08 01:29:42
Elapsed	1 day 10:45:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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--------------------
39428 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign.gz 
opened /tmp/24302.1.amd.q/RtmpodceXo/SRR1370897_1.nodup.pr2.tagAlign9b0c35e2ace4
done. read 8412294 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/24302.1.amd.q/RtmpodceXo/input15MReadsNSCLess1.05.50MSubsample.tagAlign9b0c445ab7dd
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1060745 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.125765598262468 
Top 3 estimates for fragment length 145 
Window half size 245 
Phantom peak location 55 
Phantom peak Correlation 0.114677 
Normalized Strand cross-correlation coefficient (NSC) 1.185635 
Relative Strand cross-correlation Coefficient (RSC) 2.288998 
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= 6.046463  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1653859  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000063 
Detected 223672 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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2588	2832	.	0	.	28.4436509082301	-1	3.2612628687925	122

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2588	2832	.	0	.	28.4436509082301	-1	3.2612628687925	122

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24303

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

Start	2017-01-06 14:44:39
End	2017-01-06 15:47:34
Elapsed	01:02:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_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--------------------
39429 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:45:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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 14:45:01: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:45:01: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:45:09:  1000000 
INFO  @ Fri, 06 Jan 2017 14:45:17:  2000000 
INFO  @ Fri, 06 Jan 2017 14:45:26:  3000000 
INFO  @ Fri, 06 Jan 2017 14:45:34:  4000000 
INFO  @ Fri, 06 Jan 2017 14:45:42:  5000000 
INFO  @ Fri, 06 Jan 2017 14:45:50:  6000000 
INFO  @ Fri, 06 Jan 2017 14:45:58:  7000000 
INFO  @ Fri, 06 Jan 2017 14:46:06:  8000000 
INFO  @ Fri, 06 Jan 2017 14:46:11: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:46:19:  1000000 
INFO  @ Fri, 06 Jan 2017 14:46:27:  2000000 
INFO  @ Fri, 06 Jan 2017 14:46:34:  3000000 
INFO  @ Fri, 06 Jan 2017 14:46:42:  4000000 
INFO  @ Fri, 06 Jan 2017 14:46:50:  5000000 
INFO  @ Fri, 06 Jan 2017 14:46:58:  6000000 
INFO  @ Fri, 06 Jan 2017 14:47:07:  7000000 
INFO  @ Fri, 06 Jan 2017 14:47:14:  8000000 
INFO  @ Fri, 06 Jan 2017 14:47:22:  9000000 
INFO  @ Fri, 06 Jan 2017 14:47:30:  10000000 
INFO  @ Fri, 06 Jan 2017 14:47:38:  11000000 
INFO  @ Fri, 06 Jan 2017 14:47:46:  12000000 
INFO  @ Fri, 06 Jan 2017 14:47:53:  13000000 
INFO  @ Fri, 06 Jan 2017 14:48:01:  14000000 
INFO  @ Fri, 06 Jan 2017 14:48:09:  15000000 
INFO  @ Fri, 06 Jan 2017 14:48:17:  16000000 
INFO  @ Fri, 06 Jan 2017 14:48:24:  17000000 
INFO  @ Fri, 06 Jan 2017 14:48:32:  18000000 
INFO  @ Fri, 06 Jan 2017 14:48:40:  19000000 
INFO  @ Fri, 06 Jan 2017 14:48:48:  20000000 
INFO  @ Fri, 06 Jan 2017 14:48:56:  21000000 
INFO  @ Fri, 06 Jan 2017 14:49:04:  22000000 
INFO  @ Fri, 06 Jan 2017 14:49:12:  23000000 
INFO  @ Fri, 06 Jan 2017 14:49:20:  24000000 
INFO  @ Fri, 06 Jan 2017 14:49:27:  25000000 
INFO  @ Fri, 06 Jan 2017 14:49:35:  26000000 
INFO  @ Fri, 06 Jan 2017 14:49:43:  27000000 
INFO  @ Fri, 06 Jan 2017 14:49:51:  28000000 
INFO  @ Fri, 06 Jan 2017 14:49:59:  29000000 
INFO  @ Fri, 06 Jan 2017 14:50:07:  30000000 
INFO  @ Fri, 06 Jan 2017 14:50:15:  31000000 
INFO  @ Fri, 06 Jan 2017 14:50:23:  32000000 
INFO  @ Fri, 06 Jan 2017 14:50:31:  33000000 
INFO  @ Fri, 06 Jan 2017 14:50:39:  34000000 
INFO  @ Fri, 06 Jan 2017 14:50:47:  35000000 
INFO  @ Fri, 06 Jan 2017 14:50:55:  36000000 
INFO  @ Fri, 06 Jan 2017 14:51:03:  37000000 
INFO  @ Fri, 06 Jan 2017 14:51:11:  38000000 
INFO  @ Fri, 06 Jan 2017 14:51:19:  39000000 
INFO  @ Fri, 06 Jan 2017 14:51:27:  40000000 
INFO  @ Fri, 06 Jan 2017 14:51:34:  41000000 
INFO  @ Fri, 06 Jan 2017 14:51:42:  42000000 
INFO  @ Fri, 06 Jan 2017 14:51:50:  43000000 
INFO  @ Fri, 06 Jan 2017 14:51:58:  44000000 
INFO  @ Fri, 06 Jan 2017 14:52:05:  45000000 
INFO  @ Fri, 06 Jan 2017 14:52:13:  46000000 
INFO  @ Fri, 06 Jan 2017 14:52:20:  47000000 
INFO  @ Fri, 06 Jan 2017 14:52:28:  48000000 
INFO  @ Fri, 06 Jan 2017 14:52:36:  49000000 
INFO  @ Fri, 06 Jan 2017 14:52:44:  50000000 
INFO  @ Fri, 06 Jan 2017 14:52:48: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 14:52:48: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 14:52:48: #1  total tags in treatment: 8412295 
INFO  @ Fri, 06 Jan 2017 14:52:48: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:52:48: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:52:48: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:52:48: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:52:48: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:52:48: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:52:48: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:52:48: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:01:44: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:01:44: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:01:44: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:01:44: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:01:44: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:20:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:20:25: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:20:27: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:20:29: Done! 
INFO  @ Fri, 06 Jan 2017 15:20:36: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr1/SRR1370897_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 15:20:36: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:20:36: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:20:45:  1000000 
INFO  @ Fri, 06 Jan 2017 15:20:53:  2000000 
INFO  @ Fri, 06 Jan 2017 15:21:01:  3000000 
INFO  @ Fri, 06 Jan 2017 15:21:09:  4000000 
INFO  @ Fri, 06 Jan 2017 15:21:17:  5000000 
INFO  @ Fri, 06 Jan 2017 15:21:25:  6000000 
INFO  @ Fri, 06 Jan 2017 15:21:32:  7000000 
INFO  @ Fri, 06 Jan 2017 15:21:40:  8000000 
INFO  @ Fri, 06 Jan 2017 15:21:44: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:21:52:  1000000 
INFO  @ Fri, 06 Jan 2017 15:21:59:  2000000 
INFO  @ Fri, 06 Jan 2017 15:22:07:  3000000 
INFO  @ Fri, 06 Jan 2017 15:22:15:  4000000 
INFO  @ Fri, 06 Jan 2017 15:22:22:  5000000 
INFO  @ Fri, 06 Jan 2017 15:22:30:  6000000 
INFO  @ Fri, 06 Jan 2017 15:22:37:  7000000 
INFO  @ Fri, 06 Jan 2017 15:22:44:  8000000 
INFO  @ Fri, 06 Jan 2017 15:22:52:  9000000 
INFO  @ Fri, 06 Jan 2017 15:22:59:  10000000 
INFO  @ Fri, 06 Jan 2017 15:23:07:  11000000 
INFO  @ Fri, 06 Jan 2017 15:23:14:  12000000 
INFO  @ Fri, 06 Jan 2017 15:23:21:  13000000 
INFO  @ Fri, 06 Jan 2017 15:23:28:  14000000 
INFO  @ Fri, 06 Jan 2017 15:23:36:  15000000 
INFO  @ Fri, 06 Jan 2017 15:23:43:  16000000 
INFO  @ Fri, 06 Jan 2017 15:23:50:  17000000 
INFO  @ Fri, 06 Jan 2017 15:23:58:  18000000 
INFO  @ Fri, 06 Jan 2017 15:24:05:  19000000 
INFO  @ Fri, 06 Jan 2017 15:24:13:  20000000 
INFO  @ Fri, 06 Jan 2017 15:24:20:  21000000 
INFO  @ Fri, 06 Jan 2017 15:24:27:  22000000 
INFO  @ Fri, 06 Jan 2017 15:24:35:  23000000 
INFO  @ Fri, 06 Jan 2017 15:24:42:  24000000 
INFO  @ Fri, 06 Jan 2017 15:24:49:  25000000 
INFO  @ Fri, 06 Jan 2017 15:24:57:  26000000 
INFO  @ Fri, 06 Jan 2017 15:25:04:  27000000 
INFO  @ Fri, 06 Jan 2017 15:25:11:  28000000 
INFO  @ Fri, 06 Jan 2017 15:25:18:  29000000 
INFO  @ Fri, 06 Jan 2017 15:25:25:  30000000 
INFO  @ Fri, 06 Jan 2017 15:25:33:  31000000 
INFO  @ Fri, 06 Jan 2017 15:25:40:  32000000 
INFO  @ Fri, 06 Jan 2017 15:25:47:  33000000 
INFO  @ Fri, 06 Jan 2017 15:25:55:  34000000 
INFO  @ Fri, 06 Jan 2017 15:26:02:  35000000 
INFO  @ Fri, 06 Jan 2017 15:26:09:  36000000 
INFO  @ Fri, 06 Jan 2017 15:26:17:  37000000 
INFO  @ Fri, 06 Jan 2017 15:26:24:  38000000 
INFO  @ Fri, 06 Jan 2017 15:26:32:  39000000 
INFO  @ Fri, 06 Jan 2017 15:26:39:  40000000 
INFO  @ Fri, 06 Jan 2017 15:26:46:  41000000 
INFO  @ Fri, 06 Jan 2017 15:26:53:  42000000 
INFO  @ Fri, 06 Jan 2017 15:27:01:  43000000 
INFO  @ Fri, 06 Jan 2017 15:27:08:  44000000 
INFO  @ Fri, 06 Jan 2017 15:27:15:  45000000 
INFO  @ Fri, 06 Jan 2017 15:27:22:  46000000 
INFO  @ Fri, 06 Jan 2017 15:27:29:  47000000 
INFO  @ Fri, 06 Jan 2017 15:27:37:  48000000 
INFO  @ Fri, 06 Jan 2017 15:27:44:  49000000 
INFO  @ Fri, 06 Jan 2017 15:27:51:  50000000 
INFO  @ Fri, 06 Jan 2017 15:27:55: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:27:55: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:27:55: #1  total tags in treatment: 8412295 
INFO  @ Fri, 06 Jan 2017 15:27:55: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:27:55: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:27:55: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:27:55: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:27:55: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:27:55: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:27:55: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:27:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:36:32: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:45:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:46:21: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:46:41: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:46:57: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24339

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

Start	2017-01-06 15:47:37
End	2017-01-06 16:04:34
Elapsed	00:16:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_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--------------------
566 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:47:54: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 15:47:54: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:47:54: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:47:56:  1000000 
INFO  @ Fri, 06 Jan 2017 15:47:58:  2000000 
INFO  @ Fri, 06 Jan 2017 15:48:00:  3000000 
INFO  @ Fri, 06 Jan 2017 15:48:01:  4000000 
INFO  @ Fri, 06 Jan 2017 15:48:03:  5000000 
INFO  @ Fri, 06 Jan 2017 15:48:05:  6000000 
INFO  @ Fri, 06 Jan 2017 15:48:06:  7000000 
INFO  @ Fri, 06 Jan 2017 15:48:08:  8000000 
INFO  @ Fri, 06 Jan 2017 15:48:09: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:48:11:  1000000 
INFO  @ Fri, 06 Jan 2017 15:48:12:  2000000 
INFO  @ Fri, 06 Jan 2017 15:48:14:  3000000 
INFO  @ Fri, 06 Jan 2017 15:48:16:  4000000 
INFO  @ Fri, 06 Jan 2017 15:48:17:  5000000 
INFO  @ Fri, 06 Jan 2017 15:48:19:  6000000 
INFO  @ Fri, 06 Jan 2017 15:48:20:  7000000 
INFO  @ Fri, 06 Jan 2017 15:48:22:  8000000 
INFO  @ Fri, 06 Jan 2017 15:48:24:  9000000 
INFO  @ Fri, 06 Jan 2017 15:48:26:  10000000 
INFO  @ Fri, 06 Jan 2017 15:48:27:  11000000 
INFO  @ Fri, 06 Jan 2017 15:48:29:  12000000 
INFO  @ Fri, 06 Jan 2017 15:48:30:  13000000 
INFO  @ Fri, 06 Jan 2017 15:48:32:  14000000 
INFO  @ Fri, 06 Jan 2017 15:48:34:  15000000 
INFO  @ Fri, 06 Jan 2017 15:48:35:  16000000 
INFO  @ Fri, 06 Jan 2017 15:48:37:  17000000 
INFO  @ Fri, 06 Jan 2017 15:48:39:  18000000 
INFO  @ Fri, 06 Jan 2017 15:48:40:  19000000 
INFO  @ Fri, 06 Jan 2017 15:48:42:  20000000 
INFO  @ Fri, 06 Jan 2017 15:48:43:  21000000 
INFO  @ Fri, 06 Jan 2017 15:48:45:  22000000 
INFO  @ Fri, 06 Jan 2017 15:48:47:  23000000 
INFO  @ Fri, 06 Jan 2017 15:48:48:  24000000 
INFO  @ Fri, 06 Jan 2017 15:48:50:  25000000 
INFO  @ Fri, 06 Jan 2017 15:48:51:  26000000 
INFO  @ Fri, 06 Jan 2017 15:48:53:  27000000 
INFO  @ Fri, 06 Jan 2017 15:48:55:  28000000 
INFO  @ Fri, 06 Jan 2017 15:48:56:  29000000 
INFO  @ Fri, 06 Jan 2017 15:48:58:  30000000 
INFO  @ Fri, 06 Jan 2017 15:48:59:  31000000 
INFO  @ Fri, 06 Jan 2017 15:49:01:  32000000 
INFO  @ Fri, 06 Jan 2017 15:49:03:  33000000 
INFO  @ Fri, 06 Jan 2017 15:49:04:  34000000 
INFO  @ Fri, 06 Jan 2017 15:49:06:  35000000 
INFO  @ Fri, 06 Jan 2017 15:49:08:  36000000 
INFO  @ Fri, 06 Jan 2017 15:49:09:  37000000 
INFO  @ Fri, 06 Jan 2017 15:49:11:  38000000 
INFO  @ Fri, 06 Jan 2017 15:49:12:  39000000 
INFO  @ Fri, 06 Jan 2017 15:49:14:  40000000 
INFO  @ Fri, 06 Jan 2017 15:49:16:  41000000 
INFO  @ Fri, 06 Jan 2017 15:49:17:  42000000 
INFO  @ Fri, 06 Jan 2017 15:49:19:  43000000 
INFO  @ Fri, 06 Jan 2017 15:49:21:  44000000 
INFO  @ Fri, 06 Jan 2017 15:49:22:  45000000 
INFO  @ Fri, 06 Jan 2017 15:49:24:  46000000 
INFO  @ Fri, 06 Jan 2017 15:49:25:  47000000 
INFO  @ Fri, 06 Jan 2017 15:49:27:  48000000 
INFO  @ Fri, 06 Jan 2017 15:49:28:  49000000 
INFO  @ Fri, 06 Jan 2017 15:49:30:  50000000 
INFO  @ Fri, 06 Jan 2017 15:49:32: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:49:32: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:49:32: #1  total tags in treatment: 8412294 
INFO  @ Fri, 06 Jan 2017 15:49:32: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:49:32: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:49:32: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:49:32: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:49:32: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:49:32: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:49:32: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:49:32: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:52:24: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:52:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:52:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:52:24: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:52:24: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:57:20: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:57:21: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:57:21: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:57:22: Done! 
INFO  @ Fri, 06 Jan 2017 15:57:25: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 15:57:25: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:57:25: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:57:27:  1000000 
INFO  @ Fri, 06 Jan 2017 15:57:29:  2000000 
INFO  @ Fri, 06 Jan 2017 15:57:30:  3000000 
INFO  @ Fri, 06 Jan 2017 15:57:32:  4000000 
INFO  @ Fri, 06 Jan 2017 15:57:34:  5000000 
INFO  @ Fri, 06 Jan 2017 15:57:35:  6000000 
INFO  @ Fri, 06 Jan 2017 15:57:37:  7000000 
INFO  @ Fri, 06 Jan 2017 15:57:39:  8000000 
INFO  @ Fri, 06 Jan 2017 15:57:40: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:57:42:  1000000 
INFO  @ Fri, 06 Jan 2017 15:57:43:  2000000 
INFO  @ Fri, 06 Jan 2017 15:57:45:  3000000 
INFO  @ Fri, 06 Jan 2017 15:57:46:  4000000 
INFO  @ Fri, 06 Jan 2017 15:57:48:  5000000 
INFO  @ Fri, 06 Jan 2017 15:57:50:  6000000 
INFO  @ Fri, 06 Jan 2017 15:57:51:  7000000 
INFO  @ Fri, 06 Jan 2017 15:57:53:  8000000 
INFO  @ Fri, 06 Jan 2017 15:57:54:  9000000 
INFO  @ Fri, 06 Jan 2017 15:57:56:  10000000 
INFO  @ Fri, 06 Jan 2017 15:57:57:  11000000 
INFO  @ Fri, 06 Jan 2017 15:57:59:  12000000 
INFO  @ Fri, 06 Jan 2017 15:58:00:  13000000 
INFO  @ Fri, 06 Jan 2017 15:58:02:  14000000 
INFO  @ Fri, 06 Jan 2017 15:58:04:  15000000 
INFO  @ Fri, 06 Jan 2017 15:58:05:  16000000 
INFO  @ Fri, 06 Jan 2017 15:58:07:  17000000 
INFO  @ Fri, 06 Jan 2017 15:58:09:  18000000 
INFO  @ Fri, 06 Jan 2017 15:58:10:  19000000 
INFO  @ Fri, 06 Jan 2017 15:58:12:  20000000 
INFO  @ Fri, 06 Jan 2017 15:58:13:  21000000 
INFO  @ Fri, 06 Jan 2017 15:58:15:  22000000 
INFO  @ Fri, 06 Jan 2017 15:58:16:  23000000 
INFO  @ Fri, 06 Jan 2017 15:58:18:  24000000 
INFO  @ Fri, 06 Jan 2017 15:58:19:  25000000 
INFO  @ Fri, 06 Jan 2017 15:58:21:  26000000 
INFO  @ Fri, 06 Jan 2017 15:58:23:  27000000 
INFO  @ Fri, 06 Jan 2017 15:58:24:  28000000 
INFO  @ Fri, 06 Jan 2017 15:58:26:  29000000 
INFO  @ Fri, 06 Jan 2017 15:58:27:  30000000 
INFO  @ Fri, 06 Jan 2017 15:58:29:  31000000 
INFO  @ Fri, 06 Jan 2017 15:58:30:  32000000 
INFO  @ Fri, 06 Jan 2017 15:58:32:  33000000 
INFO  @ Fri, 06 Jan 2017 15:58:33:  34000000 
INFO  @ Fri, 06 Jan 2017 15:58:35:  35000000 
INFO  @ Fri, 06 Jan 2017 15:58:37:  36000000 
INFO  @ Fri, 06 Jan 2017 15:58:38:  37000000 
INFO  @ Fri, 06 Jan 2017 15:58:40:  38000000 
INFO  @ Fri, 06 Jan 2017 15:58:41:  39000000 
INFO  @ Fri, 06 Jan 2017 15:58:43:  40000000 
INFO  @ Fri, 06 Jan 2017 15:58:44:  41000000 
INFO  @ Fri, 06 Jan 2017 15:58:46:  42000000 
INFO  @ Fri, 06 Jan 2017 15:58:47:  43000000 
INFO  @ Fri, 06 Jan 2017 15:58:49:  44000000 
INFO  @ Fri, 06 Jan 2017 15:58:51:  45000000 
INFO  @ Fri, 06 Jan 2017 15:58:52:  46000000 
INFO  @ Fri, 06 Jan 2017 15:58:54:  47000000 
INFO  @ Fri, 06 Jan 2017 15:58:55:  48000000 
INFO  @ Fri, 06 Jan 2017 15:58:57:  49000000 
INFO  @ Fri, 06 Jan 2017 15:58:58:  50000000 
INFO  @ Fri, 06 Jan 2017 15:59:00: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:59:00: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:59:00: #1  total tags in treatment: 8412294 
INFO  @ Fri, 06 Jan 2017 15:59:00: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:59:00: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:59:00: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:59:00: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:59:00: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:59:00: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:59:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:59:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 16:01:26: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 16:03:59: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 16:04:05: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 16:04:10: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 16:04:16: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24406

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

Start	2017-01-08 01:29:44
End	2017-01-08 01:31:08
Elapsed	00:01:24
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_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--------------------
46373 (process ID) old priority 0, new priority 10
Waiting for 56 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	3181	3425	.	0	.	23.2994651818338	-1	3.52207368618481	122

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	3181	3425	.	0	.	23.2994651818338	-1	3.52207368618481	122

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2588	2832	.	0	.	28.4436509082301	-1	3.2612628687925	122

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2588	2832	.	0	.	28.4436509082301	-1	3.2612628687925	122

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL383555.2	197085	197329	.	0	.	6.94102109770696	-1	3.14199564894382	122

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
GL383555.2	197085	197329	.	0	.	6.94102109770696	-1	3.14199564894382	122

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24407

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

Start	2017-01-08 01:31:09
End	2017-01-08 01:32:22
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370897_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370897_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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--------------------
46477 (process ID) old priority 0, new priority 10
Waiting for 2 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.39 1.28 0.87 0.26]
Number of reported peaks - 34296/34296 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 3941/34296 (11.5%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24408

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

Start	2017-01-08 01:32:23
End	2017-01-08 01:33:37
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/qc/ZNF574_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/ZNF574/out/qc/ZNF574_IDR_final.qc

# SYS command. line 224

 echo -e "0\t86	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/qc/ZNF574_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--------------------
46624 (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	3254

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

Start	2017-01-08 01:33:40
End	2017-01-08 01:34:48
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_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/ZNF574/out/peak/spp/rep1/SRR1370897_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--------------------
3259 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3203	3447	.	0	.	35.5338705952906	-1	3.85871761486029	122

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/rep1/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3203	3447	.	0	.	35.5338705952906	-1	3.85871761486029	122

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	6999

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

Start	2017-01-08 01:34:49
End	2017-01-08 01:34:58
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/spp/overlap/SRR1370897_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/ZNF574/out/peak/spp/overlap/SRR1370897_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
7005 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	7671

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

Start	2017-01-08 01:34:59
End	2017-01-08 01:35:07
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_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/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/peak/idr/pseudo_reps/rep1/ZNF574_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
7675 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	8223

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

Start	2017-01-08 01:35:08
End	2017-01-08 01:35:16
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/report/ZNF574_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/report/ZNF574_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/report/ZNF574_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
8227 (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, ZNF574, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF574/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF574/out/align/rep1/SRR1370897_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/ZNF574
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/ZNF574
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	23899.ZNF574.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