module load java; java -Xmx40G -jar juicer_tools.jar pre /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/01-Dinoflagellata-Kryptoperidinium_triquetrum/juicer-hifiasm.hic.p_ctg/aligned/merged_nodups.txt /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/01-Dinoflagellata-Kryptoperidinium_triquetrum/juicer-hifiasm.hic.p_ctg/aligned/inter_rerun.hic /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/01-Dinoflagellata-Kryptoperidinium_triquetrum/hifiasm.hic.p_ctg.chrom.sizes