export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/bwa-0.7.5a; module load system; module load parallel/20180122; module load java; export PATH=$PATH:/oak/stanford/groups/akundaje/marinovg/programs/juicer_tools.1.8.9/; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/06-Trypanosoma_cruzi-SRR11803985/juicer-Trypanosoma_cruzi_Dm25-ASM3648588v1 -d /oak/stanford/groups/akundaje/marinovg/papers/2024_ToL_Hi-C/2023-07-09/06-Trypanosoma_cruzi-SRR11803985/juicer-Trypanosoma_cruzi_Dm25-ASM3648588v1 -p /oak/stanford/groups/akundaje/marinovg/genomes/Kinetoplastida/Trypanosoma_cruzi_Dm25-ASM3648588v1/Trypanosoma_cruzi_Dm25-ASM3648588v1.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Kinetoplastida/Trypanosoma_cruzi_Dm25-ASM3648588v1/bwa-indexes/Trypanosoma_cruzi_Dm25-ASM3648588v1_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Kinetoplastida/Trypanosoma_cruzi_Dm25-ASM3648588v1/bwa-indexes/Trypanosoma_cruzi_Dm25-ASM3648588v1.fa