is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_939623385/Scripture-ZNF274-K562-Rep1.relaxed.narrowPeak_939623385 :  20063 peaks
 20063 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_939623385/Scripture-ZNF274-K562-Rep2.relaxed.narrowPeak_939623385 :  29853 peaks
 29853  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/Scripture/idr/Scripture-ZNF274-K562-Rep1_VS_Scripture-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-ZNF274-K562-Rep1_VS_Scripture-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_939623385/Scripture-ZNF274-K562-Rep1.relaxed.narrowPeak_939623385
/nfs/nobackup/ensembl/akundaje/tmp/idr_939623385/Scripture-ZNF274-K562-Rep2.relaxed.narrowPeak_939623385
$p
[1] 0.3667613

$rho1
[1] 0.5334835

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-ZNF274-K562-Rep1_VS_Scripture-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] 2053.263

$x.mean2
[1] 3422.93

$y.mean1
[1] 2809.985

$y.mean2
[1] 2980.397

$x.sd1
[1] 1559.635

$x.sd2
[1] 1543.323

$y.sd1
[1] 1691.025

$y.sd2
[1] 1677.382