is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_20421858/BELT-CTCF-GM12878-Rep1.relaxed.narrowPeak_20421858 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_20421858/BELT-CTCF-GM12878-Rep2.relaxed.narrowPeak_20421858 :  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-CTCF-GM12878-Rep1_VS_BELT-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-CTCF-GM12878-Rep1_VS_BELT-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_20421858/BELT-CTCF-GM12878-Rep1.relaxed.narrowPeak_20421858
/nfs/nobackup/ensembl/akundaje/tmp/idr_20421858/BELT-CTCF-GM12878-Rep2.relaxed.narrowPeak_20421858
$p
[1] 0.7299556

$rho1
[1] 0.932186

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-CTCF-GM12878-Rep1_VS_BELT-CTCF-GM12878-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] 38741.14

$x.mean2
[1] 69498.52

$y.mean1
[1] 37355.16

$y.mean2
[1] 73240.34

$x.sd1
[1] 23884.93

$x.sd2
[1] 22342.02

$y.sd1
[1] 23623.24

$y.sd2
[1] 16833.47