./run-asm-pipeline.sh -r 50 --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L1364-Gonium_sp._gDNA/SPAdes-3.14-L1364-Gonium_sp._gDNA/bwa-indexes/scaffolds.fa /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-23-Novogene-NovaSeq/juicer-L1194-Gonium_pectorale_Hi-C/aligned/merged_nodups.txt &