Summarizing the parameters employed in this execution
Listing the input files: 
Input file containing the valid pairs (generated from HIC-PRO pipeline): /sf/storage/gmo/hic/out/by_Project/HiChIP/data/NR1/NR1_allValidPairs 
Input ChIP-seq peak file: /sf/storage/gmo/hic/out/by_Project/HiChIP/data/NR1/MACS2_ExtSize/out_macs2_peaks.narrowPeak 
File containing chromosome size information corresponding to the reference chromosome: /sf/storage/gmo/mirmir/data/mm10/mm10.chr.sizes 
Reference Fasta sequence File: /sf/storage/gmo/mirmir/data/mm10/mm10.fa 
Restriction Fragment File: /sf/storage/gmo/mirmir/data/mm10/mm10.MboI.bed 
Output directory which will store all the results: /sf/storage/gmo/hic/out/by_Project/HiChIP/data/NR1/FitHiChIP_2/ 
Base directory containing the HIC-PRO executable: /home/mirmir/progs/HiC-Pro_3.1.0 
Low distance threshold: 1000000 
Higher distance threshold: 20000000 
BIN_SIZE: 100000 
PREFIX (string of output files): cross_test2 
OverWrite (1 means existing files will be overwritten): 1