./run-asm-pipeline.sh --rounds 100 --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/genomes/Heterolobosea/Naegleria_gruberi_v1.0/bwa-indexes/GCA_000004985.1_V1.0_genomic.fa /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2020-06-13-NextSeq-run/juicer-L1518-Naegleria_gruberi-Hi-C-MboI_MseI/aligned/merged_nodups.txt &