is.broadpeak FALSE 
[1] "Fix 10 stops\n"
[1] "Fix 47 stops\n"
read /broad/hptmp/anshul/idr_1195110277/dPeak3-POL2-H1ESC-Rep1.relaxed.narrowPeak_1195110277 :  120704 peaks
 120704 peaks are left after cleaning
 /broad/hptmp/anshul/idr_1195110277/dPeak3-POL2-H1ESC-Rep2.relaxed.narrowPeak_1195110277 :  145125 peaks
 145125  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-POL2-H1ESC-Rep1_VS_dPeak3-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-POL2-H1ESC-Rep1_VS_dPeak3-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_1195110277/dPeak3-POL2-H1ESC-Rep1.relaxed.narrowPeak_1195110277
/broad/hptmp/anshul/idr_1195110277/dPeak3-POL2-H1ESC-Rep2.relaxed.narrowPeak_1195110277
$p
[1] 0.5408369

$rho1
[1] 0.8388359

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-POL2-H1ESC-Rep1_VS_dPeak3-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] 20596.95

$x.mean2
[1] 37359.71

$y.mean1
[1] 19831.51

$y.mean2
[1] 38261.04

$x.sd1
[1] 14699.93

$x.sd2
[1] 13211.04

$y.sd1
[1] 14360.22

$y.sd2
[1] 12427.24