is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1435217171/Hotspotv2-GABP-GM12878-Rep1.relaxed.narrowPeak_1435217171 :  123716 peaks
 123716 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1435217171/Hotspotv2-GABP-GM12878-Rep2.relaxed.narrowPeak_1435217171 :  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/Hotspotv2/idr/Hotspotv2-GABP-GM12878-Rep1_VS_Hotspotv2-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspotv2/idr/Hotspotv2-GABP-GM12878-Rep1_VS_Hotspotv2-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1435217171/Hotspotv2-GABP-GM12878-Rep1.relaxed.narrowPeak_1435217171
/nfs/nobackup/ensembl/akundaje/tmp/idr_1435217171/Hotspotv2-GABP-GM12878-Rep2.relaxed.narrowPeak_1435217171
$p
[1] 0.7340568

$rho1
[1] 0.9285587

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspotv2/idr/Hotspotv2-GABP-GM12878-Rep1_VS_Hotspotv2-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] 10728.82

$x.mean2
[1] 17217.52

$y.mean1
[1] 10776.54

$y.mean2
[1] 17086.41

$x.sd1
[1] 7107.868

$x.sd2
[1] 4921.849

$y.sd1
[1] 7088.39

$y.sd2
[1] 5163.543