is.broadpeak FALSE 
[1] "Fix 3 stops\n"
[1] "Fix 2 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2078332054/Scripture-GABP-GM12878-Rep1.relaxed.narrowPeak_2078332054 :  12104 peaks
 12104 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2078332054/Scripture-GABP-GM12878-Rep2.relaxed.narrowPeak_2078332054 :  10682 peaks
 10682  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/Scripture/idr/Scripture-GABP-GM12878-Rep1_VS_Scripture-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-GABP-GM12878-Rep1_VS_Scripture-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2078332054/Scripture-GABP-GM12878-Rep1.relaxed.narrowPeak_2078332054
/nfs/nobackup/ensembl/akundaje/tmp/idr_2078332054/Scripture-GABP-GM12878-Rep2.relaxed.narrowPeak_2078332054
$p
[1] 0.2579871

$rho1
[1] 0.8208469

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-GABP-GM12878-Rep1_VS_Scripture-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] 1723.374

$x.mean2
[1] 1273.753

$y.mean1
[1] 1520.118

$y.mean2
[1] 1347.552

$x.sd1
[1] 706.1955

$x.sd2
[1] 804.7719

$y.sd1
[1] 766.6662

$y.sd2
[1] 813.1645