is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_150412315/Hotspotv2-P300-K562-Rep1.relaxed.narrowPeak_150412315 :  108939 peaks
 108939 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_150412315/Hotspotv2-P300-K562-Rep2.relaxed.narrowPeak_150412315 :  103439 peaks
 103439  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-P300-K562-Rep1_VS_Hotspotv2-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspotv2/idr/Hotspotv2-P300-K562-Rep1_VS_Hotspotv2-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_150412315/Hotspotv2-P300-K562-Rep1.relaxed.narrowPeak_150412315
/nfs/nobackup/ensembl/akundaje/tmp/idr_150412315/Hotspotv2-P300-K562-Rep2.relaxed.narrowPeak_150412315
$p
[1] 0.7549667

$rho1
[1] 0.8185889

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspotv2/idr/Hotspotv2-P300-K562-Rep1_VS_Hotspotv2-P300-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] 19753.51

$x.mean2
[1] 31162.45

$y.mean1
[1] 20257.9

$y.mean2
[1] 29613.09

$x.sd1
[1] 12659.19

$x.sd2
[1] 9991.478

$y.sd1
[1] 12858.63

$y.sd2
[1] 10787.42