./run-asm-pipeline.sh --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1523-Killifish-Hi-C/juicer-L1523-Killifish-Hi-C-additional_reads-against_scaffolding-3D_DNA/final-post-review/bwa-indexes/GCA_001465895.2_Nfu_20140520_genomic.FINAL.FINAL.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2021-05-03-killifish-figures/juicer-L1523-Killifish-Hi-C-all_reads_final_assembly/aligned/merged_nodups.txt &