is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_135951396/Hotspotv2-POL2-H1ESC-Rep1.relaxed.narrowPeak_135951396 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_135951396/Hotspotv2-POL2-H1ESC-Rep2.relaxed.narrowPeak_135951396 :  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/Hotspotv2/idr/Hotspotv2-POL2-H1ESC-Rep1_VS_Hotspotv2-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspotv2/idr/Hotspotv2-POL2-H1ESC-Rep1_VS_Hotspotv2-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_135951396/Hotspotv2-POL2-H1ESC-Rep1.relaxed.narrowPeak_135951396
/nfs/nobackup/ensembl/akundaje/tmp/idr_135951396/Hotspotv2-POL2-H1ESC-Rep2.relaxed.narrowPeak_135951396
$p
[1] 0.5691755

$rho1
[1] 0.8783173

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspotv2/idr/Hotspotv2-POL2-H1ESC-Rep1_VS_Hotspotv2-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] 24106.29

$x.mean2
[1] 46039.71

$y.mean1
[1] 23984.48

$y.mean2
[1] 46200.56

$x.sd1
[1] 17339.39

$x.sd2
[1] 14142.53

$y.sd1
[1] 17229.7

$y.sd2
[1] 14068.29