is.broadpeak FALSE 
[1] "Fix 31 stops\n"
[1] "Fix 10 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2712729525/GPS-GABP-GM12878-Rep1.relaxed.narrowPeak_2712729525 :  36116 peaks
 36116 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2712729525/GPS-GABP-GM12878-Rep2.relaxed.narrowPeak_2712729525 :  14576 peaks
 14576  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-GM12878-Rep1_VS_GPS-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-GABP-GM12878-Rep1_VS_GPS-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2712729525/GPS-GABP-GM12878-Rep1.relaxed.narrowPeak_2712729525
/nfs/nobackup/ensembl/akundaje/tmp/idr_2712729525/GPS-GABP-GM12878-Rep2.relaxed.narrowPeak_2712729525
$p
[1] 0.8215903

$rho1
[1] 0.9381609

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-GABP-GM12878-Rep1_VS_GPS-GABP-GM12878-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] 3624.935

$x.mean2
[1] 6486.952

$y.mean1
[1] 3611.156

$y.mean2
[1] 6548.781

$x.sd1
[1] 2257.855

$x.sd2
[1] 1367.786

$y.sd1
[1] 2241.188

$y.sd2
[1] 1359.683