is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_111826383/MOSAiCS-POL2-H1ESC-Rep1.relaxed.narrowPeak_111826383 :  107340 peaks
 107340 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_111826383/MOSAiCS-POL2-H1ESC-Rep2.relaxed.narrowPeak_111826383 :  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-POL2-H1ESC-Rep1_VS_MOSAiCS-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-POL2-H1ESC-Rep1_VS_MOSAiCS-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_111826383/MOSAiCS-POL2-H1ESC-Rep1.relaxed.narrowPeak_111826383
/nfs/nobackup/ensembl/akundaje/tmp/idr_111826383/MOSAiCS-POL2-H1ESC-Rep2.relaxed.narrowPeak_111826383
$p
[1] 0.5524452

$rho1
[1] 0.8837245

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-POL2-H1ESC-Rep1_VS_MOSAiCS-POL2-H1ESC-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] 22338.31

$x.mean2
[1] 42245.4

$y.mean1
[1] 23254.52

$y.mean2
[1] 41114.84

$x.sd1
[1] 16600.31

$x.sd2
[1] 12961.5

$y.sd1
[1] 17073.69

$y.sd2
[1] 13821.33