is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_15589900/BELT-POL2-H1ESC-Rep1.relaxed.narrowPeak_15589900 :  105332 peaks
 105332 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_15589900/BELT-POL2-H1ESC-Rep2.relaxed.narrowPeak_15589900 :  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/BELT/idr/BELT-POL2-H1ESC-Rep1_VS_BELT-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-POL2-H1ESC-Rep1_VS_BELT-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_15589900/BELT-POL2-H1ESC-Rep1.relaxed.narrowPeak_15589900
/nfs/nobackup/ensembl/akundaje/tmp/idr_15589900/BELT-POL2-H1ESC-Rep2.relaxed.narrowPeak_15589900
$p
[1] 0.5958252

$rho1
[1] 0.7690071

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-POL2-H1ESC-Rep1_VS_BELT-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] 23919.78

$x.mean2
[1] 46637.51

$y.mean1
[1] 24412.52

$y.mean2
[1] 45911.57

$x.sd1
[1] 16641.28

$x.sd2
[1] 13704.22

$y.sd1
[1] 17006.69

$y.sd2
[1] 14205.28