./run-asm-pipeline.sh --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/genomes/Diatomes/Phaeodactylum_tricornutum-ASM15095v2/bwa-indexes/Phaeodactylum_tricornutum.ASM15095v2.20+chrM.fa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-05-15-NextSeq-run/juicer-L1355-Phaeodactylum_tricoturnum-HiC-MboI_MluCI-all_reads/aligned/merged_nodups.txt &