is.broadpeak FALSE 
[1] "Fix 39 stops\n"
[1] "Fix 85 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_254806596/GPS-POL2-H1ESC-Rep1.relaxed.narrowPeak_254806596 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_254806596/GPS-POL2-H1ESC-Rep2.relaxed.narrowPeak_254806596 :  125000 peaks
 125000  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/GPS/idr/GPS-POL2-H1ESC-Rep1_VS_GPS-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-POL2-H1ESC-Rep1_VS_GPS-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_254806596/GPS-POL2-H1ESC-Rep1.relaxed.narrowPeak_254806596
/nfs/nobackup/ensembl/akundaje/tmp/idr_254806596/GPS-POL2-H1ESC-Rep2.relaxed.narrowPeak_254806596
$p
[1] 0.6168958

$rho1
[1] 0.8505917

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-POL2-H1ESC-Rep1_VS_GPS-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] 23864.37

$x.mean2
[1] 43870.51

$y.mean1
[1] 23275.76

$y.mean2
[1] 44817.59

$x.sd1
[1] 16550.34

$x.sd2
[1] 13299.12

$y.sd1
[1] 16322.53

$y.sd2
[1] 12229.76