is.broadpeak FALSE 
[1] "Fix 46 stops\n"
[1] "Fix 53 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2262815281/dPeak-POL2-H1ESC-Rep1.relaxed.narrowPeak_2262815281 :  121599 peaks
 121599 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2262815281/dPeak-POL2-H1ESC-Rep2.relaxed.narrowPeak_2262815281 :  125000 peaks
 125000  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-POL2-H1ESC-Rep1_VS_dPeak-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-POL2-H1ESC-Rep1_VS_dPeak-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2262815281/dPeak-POL2-H1ESC-Rep1.relaxed.narrowPeak_2262815281
/nfs/nobackup/ensembl/akundaje/tmp/idr_2262815281/dPeak-POL2-H1ESC-Rep2.relaxed.narrowPeak_2262815281
$p
[1] 0.5777989

$rho1
[1] 0.7534545

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-POL2-H1ESC-Rep1_VS_dPeak-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] 17634.86

$x.mean2
[1] 30627.41

$y.mean1
[1] 17572.89

$y.mean2
[1] 30712.15

$x.sd1
[1] 12327.78

$x.sd2
[1] 10792.34

$y.sd1
[1] 12325.22

$y.sd2
[1] 10693.28