is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_292211063/Hotspot-P300-K562-Rep1.relaxed.narrowPeak_292211063 :  108939 peaks
 108939 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_292211063/Hotspot-P300-K562-Rep2.relaxed.narrowPeak_292211063 :  103439 peaks
 103439  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-P300-K562-Rep1_VS_Hotspot-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-P300-K562-Rep1_VS_Hotspot-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_292211063/Hotspot-P300-K562-Rep1.relaxed.narrowPeak_292211063
/nfs/nobackup/ensembl/akundaje/tmp/idr_292211063/Hotspot-P300-K562-Rep2.relaxed.narrowPeak_292211063
$p
[1] 0.6145107

$rho1
[1] 0.7827033

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-P300-K562-Rep1_VS_Hotspot-P300-K562-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] 17415.15

$x.mean2
[1] 30741.03

$y.mean1
[1] 17777

$y.mean2
[1] 30164.82

$x.sd1
[1] 11889.7

$x.sd2
[1] 10261.81

$y.sd1
[1] 12326.46

$y.sd2
[1] 10162.64