./run-asm-pipeline.sh --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L1368-Galdieria_sulphuraria_gDNA/SPAdes-3.14-L1368-Galdieria_sulphuraria_gDNA/bwa-indexes/scaffolds.fa /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-23-Novogene-NovaSeq/juicer-L1112-Galdieria_sulphuraria_Hi-C/aligned/merged_nodups.txt &