is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_26831482/GEMv2-ZNF274-K562-Rep1.relaxed.narrowPeak_26831482 :  840 peaks
 840 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_26831482/GEMv2-ZNF274-K562-Rep2.relaxed.narrowPeak_26831482 :  1389 peaks
 1389  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/GEMv2/idr/GEMv2-ZNF274-K562-Rep1_VS_GEMv2-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-ZNF274-K562-Rep1_VS_GEMv2-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_26831482/GEMv2-ZNF274-K562-Rep1.relaxed.narrowPeak_26831482
/nfs/nobackup/ensembl/akundaje/tmp/idr_26831482/GEMv2-ZNF274-K562-Rep2.relaxed.narrowPeak_26831482
$p
[1] 0.7328891

$rho1
[1] 0.8901062

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-ZNF274-K562-Rep1_VS_GEMv2-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] 102.745

$x.mean2
[1] 127.3346

$y.mean1
[1] 108.9644

$y.mean2
[1] 115.2312

$x.sd1
[1] 61.92759

$x.sd2
[1] 65.50629

$y.sd1
[1] 66.44809

$y.sd2
[1] 59.45754