is.broadpeak FALSE 
[1] "Fix 63 stops\n"
[1] "Fix 54 stops\n"
read /broad/hptmp/anshul/idr_833015338/dPeak3-GABP-GM12878-Rep1.relaxed.narrowPeak_833015338 :  116780 peaks
 116780 peaks are left after cleaning
 /broad/hptmp/anshul/idr_833015338/dPeak3-GABP-GM12878-Rep2.relaxed.narrowPeak_833015338 :  146602 peaks
 146602  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-GABP-GM12878-Rep1_VS_dPeak3-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-GABP-GM12878-Rep1_VS_dPeak3-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_833015338/dPeak3-GABP-GM12878-Rep1.relaxed.narrowPeak_833015338
/broad/hptmp/anshul/idr_833015338/dPeak3-GABP-GM12878-Rep2.relaxed.narrowPeak_833015338
$p
[1] 0.535031

$rho1
[1] 0.8860387

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-GABP-GM12878-Rep1_VS_dPeak3-GABP-GM12878-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] 11340.05

$x.mean2
[1] 21627.5

$y.mean1
[1] 11300.9

$y.mean2
[1] 21672.53

$x.sd1
[1] 8415.713

$x.sd2
[1] 6944.088

$y.sd1
[1] 8181.899

$y.sd2
[1] 7194.004