is.broadpeak FALSE 
read /broad/hptmp/anshul/idr_830324863/MOSAiCS3-GABP-GM12878-Rep1.relaxed.narrowPeak_830324863 :  103697 peaks
 103697 peaks are left after cleaning
 /broad/hptmp/anshul/idr_830324863/MOSAiCS3-GABP-GM12878-Rep2.relaxed.narrowPeak_830324863 :  125505 peaks
 125505  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-GABP-GM12878-Rep1_VS_MOSAiCS3-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-GABP-GM12878-Rep1_VS_MOSAiCS3-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_830324863/MOSAiCS3-GABP-GM12878-Rep1.relaxed.narrowPeak_830324863
/broad/hptmp/anshul/idr_830324863/MOSAiCS3-GABP-GM12878-Rep2.relaxed.narrowPeak_830324863
$p
[1] 0.3788711

$rho1
[1] 0.9152756

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-GABP-GM12878-Rep1_VS_MOSAiCS3-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] 10182.05

$x.mean2
[1] 20290.51

$y.mean1
[1] 10410.92

$y.mean2
[1] 20150.69

$x.sd1
[1] 8795.369

$x.sd2
[1] 7705.595

$y.sd1
[1] 8504.874

$y.sd2
[1] 8075.99