is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_123308799/Hotspot-GABP-GM12878-Rep1.relaxed.narrowPeak_123308799 :  123716 peaks
 123716 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_123308799/Hotspot-GABP-GM12878-Rep2.relaxed.narrowPeak_123308799 :  76546 peaks
 76546  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-GABP-GM12878-Rep1_VS_Hotspot-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-GABP-GM12878-Rep1_VS_Hotspot-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_123308799/Hotspot-GABP-GM12878-Rep1.relaxed.narrowPeak_123308799
/nfs/nobackup/ensembl/akundaje/tmp/idr_123308799/Hotspot-GABP-GM12878-Rep2.relaxed.narrowPeak_123308799
$p
[1] 0.4881421

$rho1
[1] 0.9233264

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-GABP-GM12878-Rep1_VS_Hotspot-GABP-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] 8406.211

$x.mean2
[1] 16327.7

$y.mean1
[1] 8137.695

$y.mean2
[1] 16583.82

$x.sd1
[1] 6531.431

$x.sd2
[1] 5456.192

$y.sd1
[1] 6320.734

$y.sd2
[1] 5306.68