is.broadpeak FALSE 
read /broad/hptmp/anshul/idr_604410179/MOSAiCS3-POL2-H1ESC-Rep1.relaxed.narrowPeak_604410179 :  106812 peaks
 106812 peaks are left after cleaning
 /broad/hptmp/anshul/idr_604410179/MOSAiCS3-POL2-H1ESC-Rep2.relaxed.narrowPeak_604410179 :  125250 peaks
 125250  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-POL2-H1ESC-Rep1_VS_MOSAiCS3-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-POL2-H1ESC-Rep1_VS_MOSAiCS3-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_604410179/MOSAiCS3-POL2-H1ESC-Rep1.relaxed.narrowPeak_604410179
/broad/hptmp/anshul/idr_604410179/MOSAiCS3-POL2-H1ESC-Rep2.relaxed.narrowPeak_604410179
$p
[1] 0.5010146

$rho1
[1] 0.9252702

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-POL2-H1ESC-Rep1_VS_MOSAiCS3-POL2-H1ESC-Rep2-overlapped-peaks.txt
Write number of peaks above IDR cutoff [0.01, 0.25]: npeaks-aboveIDR.txt
Marginal mean of two components:
$x.mean1
[1] 19170.33

$x.mean2
[1] 37463.7

$y.mean1
[1] 19647.19

$y.mean2
[1] 36984.91

$x.sd1
[1] 15080.49

$x.sd2
[1] 11780.44

$y.sd1
[1] 15242.99

$y.sd2
[1] 12283.77