is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read /broad/hptmp/anshul/idr_2867530978/dPeak3-CTCF-GM12878-Rep1.relaxed.narrowPeak_2867530978 :  116262 peaks
 116262 peaks are left after cleaning
 /broad/hptmp/anshul/idr_2867530978/dPeak3-CTCF-GM12878-Rep2.relaxed.narrowPeak_2867530978 :  130822 peaks
 130822  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-CTCF-GM12878-Rep1_VS_dPeak3-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-CTCF-GM12878-Rep1_VS_dPeak3-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_2867530978/dPeak3-CTCF-GM12878-Rep1.relaxed.narrowPeak_2867530978
/broad/hptmp/anshul/idr_2867530978/dPeak3-CTCF-GM12878-Rep2.relaxed.narrowPeak_2867530978
$p
[1] 0.7075002

$rho1
[1] 0.9765525

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-CTCF-GM12878-Rep1_VS_dPeak3-CTCF-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] 33398.06

$x.mean2
[1] 63186.53

$y.mean1
[1] 32082.18

$y.mean2
[1] 66365.62

$x.sd1
[1] 20611.39

$x.sd2
[1] 19112.98

$y.sd1
[1] 20372.6

$y.sd2
[1] 13610.99