is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2442014668/MOSAiCS-ZNF274-K562-Rep1.relaxed.narrowPeak_2442014668 :  106725 peaks
 106725 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2442014668/MOSAiCS-ZNF274-K562-Rep2.relaxed.narrowPeak_2442014668 :  112607 peaks
 112607  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-ZNF274-K562-Rep1_VS_MOSAiCS-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-ZNF274-K562-Rep1_VS_MOSAiCS-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2442014668/MOSAiCS-ZNF274-K562-Rep1.relaxed.narrowPeak_2442014668
/nfs/nobackup/ensembl/akundaje/tmp/idr_2442014668/MOSAiCS-ZNF274-K562-Rep2.relaxed.narrowPeak_2442014668
$p
[1] 0.3585073

$rho1
[1] 0.841028

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-ZNF274-K562-Rep1_VS_MOSAiCS-ZNF274-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] 5532.205

$x.mean2
[1] 9183.95

$y.mean1
[1] 6744.314

$y.mean2
[1] 8503.912

$x.sd1
[1] 4496.6

$x.sd2
[1] 4012.017

$y.sd1
[1] 4498.954

$y.sd2
[1] 4445.708