is.broadpeak FALSE 
[1] "Fix 3 stops\n"
[1] "Fix 13 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2379123984/GPS-GABP-HELAS3-Rep1.relaxed.narrowPeak_2379123984 :  21010 peaks
 21010 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2379123984/GPS-GABP-HELAS3-Rep2.relaxed.narrowPeak_2379123984 :  28399 peaks
 28399  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-GABP-HELAS3-Rep1_VS_GPS-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-GABP-HELAS3-Rep1_VS_GPS-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2379123984/GPS-GABP-HELAS3-Rep1.relaxed.narrowPeak_2379123984
/nfs/nobackup/ensembl/akundaje/tmp/idr_2379123984/GPS-GABP-HELAS3-Rep2.relaxed.narrowPeak_2379123984
$p
[1] 0.627548

$rho1
[1] 0.9530059

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-GABP-HELAS3-Rep1_VS_GPS-GABP-HELAS3-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] 3669.562

$x.mean2
[1] 7386.31

$y.mean1
[1] 3727.451

$y.mean2
[1] 7289.292

$x.sd1
[1] 2572.275

$x.sd2
[1] 1754.684

$y.sd1
[1] 2633.277

$y.sd2
[1] 1803.573