is.broadpeak FALSE 
[1] "Fix 20 stops\n"
[1] "Fix 1 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_165746038/Scripture-POL2-H1ESC-Rep1.relaxed.narrowPeak_165746038 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_165746038/Scripture-POL2-H1ESC-Rep2.relaxed.narrowPeak_165746038 :  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/Scripture/idr/Scripture-POL2-H1ESC-Rep1_VS_Scripture-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-POL2-H1ESC-Rep1_VS_Scripture-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_165746038/Scripture-POL2-H1ESC-Rep1.relaxed.narrowPeak_165746038
/nfs/nobackup/ensembl/akundaje/tmp/idr_165746038/Scripture-POL2-H1ESC-Rep2.relaxed.narrowPeak_165746038
$p
[1] 0.7883901

$rho1
[1] -0.05784055

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-POL2-H1ESC-Rep1_VS_Scripture-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] 10653.98

$x.mean2
[1] 7000.259

$y.mean1
[1] 10570.73

$y.mean2
[1] 7307.734

$x.sd1
[1] 5428.893

$x.sd2
[1] 5759.799

$y.sd1
[1] 5506.566

$y.sd2
[1] 5671.404