is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2770831114/Hotspot-ZNF274-K562-Rep1.relaxed.narrowPeak_2770831114 :  71867 peaks
 71867 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2770831114/Hotspot-ZNF274-K562-Rep2.relaxed.narrowPeak_2770831114 :  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/Hotspot/idr/Hotspot-ZNF274-K562-Rep1_VS_Hotspot-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-ZNF274-K562-Rep1_VS_Hotspot-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2770831114/Hotspot-ZNF274-K562-Rep1.relaxed.narrowPeak_2770831114
/nfs/nobackup/ensembl/akundaje/tmp/idr_2770831114/Hotspot-ZNF274-K562-Rep2.relaxed.narrowPeak_2770831114
$p
[1] 0.4932555

$rho1
[1] 0.8022239

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-ZNF274-K562-Rep1_VS_Hotspot-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] 1705.254

$x.mean2
[1] 2976.979

$y.mean1
[1] 1731.658

$y.mean2
[1] 2951.264

$x.sd1
[1] 1314.903

$x.sd2
[1] 1073.529

$y.sd1
[1] 1188.527

$y.sd2
[1] 1234.769