is.broadpeak FALSE 
[1] "Fix 38 stops\n"
[1] "Fix 45 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1780428962/GEM-P300-K562-Rep1.relaxed.narrowPeak_1780428962 :  78860 peaks
 78860 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1780428962/GEM-P300-K562-Rep2.relaxed.narrowPeak_1780428962 :  92666 peaks
 92666  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/GEM/idr/GEM-P300-K562-Rep1_VS_GEM-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-P300-K562-Rep1_VS_GEM-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1780428962/GEM-P300-K562-Rep1.relaxed.narrowPeak_1780428962
/nfs/nobackup/ensembl/akundaje/tmp/idr_1780428962/GEM-P300-K562-Rep2.relaxed.narrowPeak_1780428962
$p
[1] 0.7011063

$rho1
[1] 0.8230756

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-P300-K562-Rep1_VS_GEM-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] 18984.82

$x.mean2
[1] 28856.79

$y.mean1
[1] 19412.81

$y.mean2
[1] 27855.04

$x.sd1
[1] 12570.12

$x.sd2
[1] 9886.04

$y.sd1
[1] 12669.27

$y.sd2
[1] 10498.71