is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2122723437/BELT-ZNF274-K562-Rep1.relaxed.narrowPeak_2122723437 :  109402 peaks
 109402 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2122723437/BELT-ZNF274-K562-Rep2.relaxed.narrowPeak_2122723437 :  115421 peaks
 115421  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-ZNF274-K562-Rep1_VS_BELT-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-ZNF274-K562-Rep1_VS_BELT-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2122723437/BELT-ZNF274-K562-Rep1.relaxed.narrowPeak_2122723437
/nfs/nobackup/ensembl/akundaje/tmp/idr_2122723437/BELT-ZNF274-K562-Rep2.relaxed.narrowPeak_2122723437
$p
[1] 0.3341979

$rho1
[1] 0.6445174

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/BELT/idr/BELT-ZNF274-K562-Rep1_VS_BELT-ZNF274-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] 4915.153

$x.mean2
[1] 9502.993

$y.mean1
[1] 6327.759

$y.mean2
[1] 8790.638

$x.sd1
[1] 4362.09

$x.sd2
[1] 3892.624

$y.sd1
[1] 4451.449

$y.sd2
[1] 4447.244