is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_158314408/Hotspot-CTCF-GM12878-Rep1.relaxed.narrowPeak_158314408 :  96377 peaks
 96377 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_158314408/Hotspot-CTCF-GM12878-Rep2.relaxed.narrowPeak_158314408 :  102225 peaks
 102225  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/Hotspot/idr/Hotspot-CTCF-GM12878-Rep1_VS_Hotspot-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-CTCF-GM12878-Rep1_VS_Hotspot-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_158314408/Hotspot-CTCF-GM12878-Rep1.relaxed.narrowPeak_158314408
/nfs/nobackup/ensembl/akundaje/tmp/idr_158314408/Hotspot-CTCF-GM12878-Rep2.relaxed.narrowPeak_158314408
$p
[1] 0.7520393

$rho1
[1] 0.9393486

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-CTCF-GM12878-Rep1_VS_Hotspot-CTCF-GM12878-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] 31803.49

$x.mean2
[1] 58028.99

$y.mean1
[1] 30576.12

$y.mean2
[1] 61744.94

$x.sd1
[1] 19045.01

$x.sd2
[1] 18843.67

$y.sd1
[1] 18903.64

$y.sd2
[1] 12571.89