is.broadpeak FALSE 
[1] "Fix 82 stops\n"
[1] "Fix 107 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_236557623/GEM-POL2-H1NEURON-Rep1.relaxed.narrowPeak_236557623 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_236557623/GEM-POL2-H1NEURON-Rep2.relaxed.narrowPeak_236557623 :  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/GEM/idr/GEM-POL2-H1NEURON-Rep1_VS_GEM-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-POL2-H1NEURON-Rep1_VS_GEM-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_236557623/GEM-POL2-H1NEURON-Rep1.relaxed.narrowPeak_236557623
/nfs/nobackup/ensembl/akundaje/tmp/idr_236557623/GEM-POL2-H1NEURON-Rep2.relaxed.narrowPeak_236557623
$p
[1] 0.6688707

$rho1
[1] 0.8866382

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-POL2-H1NEURON-Rep1_VS_GEM-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] 29454.23

$x.mean2
[1] 56097.63

$y.mean1
[1] 29580.1

$y.mean2
[1] 55843.63

$x.sd1
[1] 19821.69

$x.sd2
[1] 14364.29

$y.sd1
[1] 20006.92

$y.sd2
[1] 14313.76