is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_256128515/MOSAiCS-POL2-H1NEURON-Rep1.relaxed.narrowPeak_256128515 :  118299 peaks
 118299 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_256128515/MOSAiCS-POL2-H1NEURON-Rep2.relaxed.narrowPeak_256128515 :  122430 peaks
 122430  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-POL2-H1NEURON-Rep1_VS_MOSAiCS-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-POL2-H1NEURON-Rep1_VS_MOSAiCS-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_256128515/MOSAiCS-POL2-H1NEURON-Rep1.relaxed.narrowPeak_256128515
/nfs/nobackup/ensembl/akundaje/tmp/idr_256128515/MOSAiCS-POL2-H1NEURON-Rep2.relaxed.narrowPeak_256128515
$p
[1] 0.6994071

$rho1
[1] 0.9152676

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-POL2-H1NEURON-Rep1_VS_MOSAiCS-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] 35362.17

$x.mean2
[1] 56941.85

$y.mean1
[1] 35941

$y.mean2
[1] 55596.56

$x.sd1
[1] 24013.12

$x.sd2
[1] 16571.88

$y.sd1
[1] 24627.04

$y.sd2
[1] 16146.21