is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_76812712/MOSAiCS-P300-K562-Rep1.relaxed.narrowPeak_76812712 :  102996 peaks
 102996 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_76812712/MOSAiCS-P300-K562-Rep2.relaxed.narrowPeak_76812712 :  125000 peaks
 125000  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-P300-K562-Rep1_VS_MOSAiCS-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-P300-K562-Rep1_VS_MOSAiCS-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_76812712/MOSAiCS-P300-K562-Rep1.relaxed.narrowPeak_76812712
/nfs/nobackup/ensembl/akundaje/tmp/idr_76812712/MOSAiCS-P300-K562-Rep2.relaxed.narrowPeak_76812712
$p
[1] 0.7598805

$rho1
[1] 0.7997887

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-P300-K562-Rep1_VS_MOSAiCS-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] 26437.16

$x.mean2
[1] 44527.01

$y.mean1
[1] 26953.29

$y.mean2
[1] 42897.45

$x.sd1
[1] 16834.83

$x.sd2
[1] 13031.14

$y.sd1
[1] 17220.1

$y.sd2
[1] 13559.02