is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_8813644/SPP-GABP-HELAS3-Rep2.relaxed.narrowPeak_8813644 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_8813644/SPP-GABP-HELAS3-Rep1.relaxed.narrowPeak_8813644 :  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-GABP-HELAS3-Rep2_VS_SPP-GABP-HELAS3-Rep1-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-GABP-HELAS3-Rep2_VS_SPP-GABP-HELAS3-Rep1-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_8813644/SPP-GABP-HELAS3-Rep2.relaxed.narrowPeak_8813644
/nfs/nobackup/ensembl/akundaje/tmp/idr_8813644/SPP-GABP-HELAS3-Rep1.relaxed.narrowPeak_8813644
$p
[1] 0.3702684

$rho1
[1] 0.9532443

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-GABP-HELAS3-Rep2_VS_SPP-GABP-HELAS3-Rep1-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] 5420.624

$x.mean2
[1] 13110.77

$y.mean1
[1] 5304.731

$y.mean2
[1] 13179.09

$x.sd1
[1] 4684.448

$x.sd2
[1] 4568.826

$y.sd1
[1] 4621.48

$y.sd2
[1] 4489.562