is.broadpeak FALSE 
[1] "Fix 13 stops\n"
[1] "Fix 23 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1283118924/Scripture-P300-K562-Rep1.relaxed.narrowPeak_1283118924 :  90058 peaks
 90058 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1283118924/Scripture-P300-K562-Rep2.relaxed.narrowPeak_1283118924 :  111836 peaks
 111836  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-P300-K562-Rep1_VS_Scripture-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-P300-K562-Rep1_VS_Scripture-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1283118924/Scripture-P300-K562-Rep1.relaxed.narrowPeak_1283118924
/nfs/nobackup/ensembl/akundaje/tmp/idr_1283118924/Scripture-P300-K562-Rep2.relaxed.narrowPeak_1283118924
$p
[1] 0.1418683

$rho1
[1] 0.8495489

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-P300-K562-Rep1_VS_Scripture-P300-K562-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] 15810.79

$x.mean2
[1] 11639.09

$y.mean1
[1] 15325.65

$y.mean2
[1] 11720.26

$x.sd1
[1] 5108.388

$x.sd2
[1] 7168.667

$y.sd1
[1] 7471.733

$y.sd2
[1] 6859.072