is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_101757192/Hotspot-GABP-HELAS3-Rep1.relaxed.narrowPeak_101757192 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_101757192/Hotspot-GABP-HELAS3-Rep2.relaxed.narrowPeak_101757192 :  110863 peaks
 110863  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-GABP-HELAS3-Rep1_VS_Hotspot-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-GABP-HELAS3-Rep1_VS_Hotspot-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_101757192/Hotspot-GABP-HELAS3-Rep1.relaxed.narrowPeak_101757192
/nfs/nobackup/ensembl/akundaje/tmp/idr_101757192/Hotspot-GABP-HELAS3-Rep2.relaxed.narrowPeak_101757192
$p
[1] 0.4141287

$rho1
[1] 0.9546424

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-GABP-HELAS3-Rep1_VS_Hotspot-GABP-HELAS3-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] 5309.604

$x.mean2
[1] 12484.59

$y.mean1
[1] 5389.498

$y.mean2
[1] 12428.01

$x.sd1
[1] 4436.845

$x.sd2
[1] 4024.747

$y.sd1
[1] 4440.153

$y.sd2
[1] 4120.919