is.broadpeak FALSE 
[1] "Fix 28 stops\n"
[1] "Fix 27 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_42361926/Scripture-POL2-H1NEURON-Rep1.relaxed.narrowPeak_42361926 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_42361926/Scripture-POL2-H1NEURON-Rep2.relaxed.narrowPeak_42361926 :  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-H1NEURON-Rep1_VS_Scripture-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-POL2-H1NEURON-Rep1_VS_Scripture-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_42361926/Scripture-POL2-H1NEURON-Rep1.relaxed.narrowPeak_42361926
/nfs/nobackup/ensembl/akundaje/tmp/idr_42361926/Scripture-POL2-H1NEURON-Rep2.relaxed.narrowPeak_42361926
$p
[1] 0.222172

$rho1
[1] 0.3599485

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-POL2-H1NEURON-Rep1_VS_Scripture-POL2-H1NEURON-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] 15584.81

$x.mean2
[1] 14779.95

$y.mean1
[1] 15411.02

$y.mean2
[1] 14829.85

$x.sd1
[1] 9638.22

$x.sd2
[1] 8316.832

$y.sd1
[1] 9214.087

$y.sd2
[1] 8457.835