is.broadpeak FALSE 
read /broad/hptmp/anshul/idr_29198373/MOSAiCS3-POL2-H1NEURON-Rep1.relaxed.narrowPeak_29198373 :  117823 peaks
 117823 peaks are left after cleaning
 /broad/hptmp/anshul/idr_29198373/MOSAiCS3-POL2-H1NEURON-Rep2.relaxed.narrowPeak_29198373 :  122229 peaks
 122229  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-POL2-H1NEURON-Rep1_VS_MOSAiCS3-POL2-H1NEURON-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-POL2-H1NEURON-Rep1_VS_MOSAiCS3-POL2-H1NEURON-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_29198373/MOSAiCS3-POL2-H1NEURON-Rep1.relaxed.narrowPeak_29198373
/broad/hptmp/anshul/idr_29198373/MOSAiCS3-POL2-H1NEURON-Rep2.relaxed.narrowPeak_29198373
$p
[1] 0.6722451

$rho1
[1] 0.9228751

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-POL2-H1NEURON-Rep1_VS_MOSAiCS3-POL2-H1NEURON-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] 32527.22

$x.mean2
[1] 55664.41

$y.mean1
[1] 33261.31

$y.mean2
[1] 54160.21

$x.sd1
[1] 22537.58

$x.sd2
[1] 15312.47

$y.sd1
[1] 23274.8

$y.sd2
[1] 15215.3