./run-asm-pipeline.sh --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L1400-Chaetoceros_gracilis_gDNA/SPAdes-3.14-L1400-Chaetoceros_gracilis_gDNA/bwa-indexes/scaffolds.fa /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-02-13-Novogene-NovaSeq/juicer-L1409-Chaetoceros_gracilis_Hi-C-MboI_MseI/aligned/merged_nodups.txt &