is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1916512059/BELT-GABP-HELAS3-Rep1.relaxed.narrowPeak_1916512059 :  101074 peaks
 101074 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1916512059/BELT-GABP-HELAS3-Rep2.relaxed.narrowPeak_1916512059 :  118606 peaks
 118606  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-GABP-HELAS3-Rep1_VS_BELT-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-GABP-HELAS3-Rep1_VS_BELT-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1916512059/BELT-GABP-HELAS3-Rep1.relaxed.narrowPeak_1916512059
/nfs/nobackup/ensembl/akundaje/tmp/idr_1916512059/BELT-GABP-HELAS3-Rep2.relaxed.narrowPeak_1916512059
$p
[1] 0.4556192

$rho1
[1] 0.8695399

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-GABP-HELAS3-Rep1_VS_BELT-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] 11492.52

$x.mean2
[1] 24055.41

$y.mean1
[1] 11396.6

$y.mean2
[1] 24135.73

$x.sd1
[1] 8887.519

$x.sd2
[1] 8224.801

$y.sd1
[1] 8872.255

$y.sd2
[1] 8114.313