is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2493914945/Hotspot-POL2-H1NEURON-Rep1.relaxed.narrowPeak_2493914945 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2493914945/Hotspot-POL2-H1NEURON-Rep2.relaxed.narrowPeak_2493914945 :  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-POL2-H1NEURON-Rep1_VS_Hotspot-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-POL2-H1NEURON-Rep1_VS_Hotspot-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2493914945/Hotspot-POL2-H1NEURON-Rep1.relaxed.narrowPeak_2493914945
/nfs/nobackup/ensembl/akundaje/tmp/idr_2493914945/Hotspot-POL2-H1NEURON-Rep2.relaxed.narrowPeak_2493914945
$p
[1] 0.6219203

$rho1
[1] 0.8872362

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Hotspot/idr/Hotspot-POL2-H1NEURON-Rep1_VS_Hotspot-POL2-H1NEURON-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] 29882.57

$x.mean2
[1] 63090.32

$y.mean1
[1] 30590.3

$y.mean2
[1] 61926.85

$x.sd1
[1] 20055.71

$x.sd2
[1] 15496.19

$y.sd1
[1] 21311.06

$y.sd2
[1] 15161.06