is.broadpeak FALSE 
[1] "Fix 17 stops\n"
[1] "Fix 7 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1405228954/SPP-POL2-H1ESC-Rep1.relaxed.narrowPeak_1405228954 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1405228954/SPP-POL2-H1ESC-Rep2.relaxed.narrowPeak_1405228954 :  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/SPP/idr/SPP-POL2-H1ESC-Rep1_VS_SPP-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-POL2-H1ESC-Rep1_VS_SPP-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1405228954/SPP-POL2-H1ESC-Rep1.relaxed.narrowPeak_1405228954
/nfs/nobackup/ensembl/akundaje/tmp/idr_1405228954/SPP-POL2-H1ESC-Rep2.relaxed.narrowPeak_1405228954
$p
[1] 0.4732653

$rho1
[1] 0.8055606

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-POL2-H1ESC-Rep1_VS_SPP-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] 18692.26

$x.mean2
[1] 36235.4

$y.mean1
[1] 19076.4

$y.mean2
[1] 35890.18

$x.sd1
[1] 14157.21

$x.sd2
[1] 12955.16

$y.sd1
[1] 14445.57

$y.sd2
[1] 13125.73