Too slow to get the inter.hic

[YouxinZhao]

I am running the juicer. sh pipeline, but it is too slow to obtain inter.hic. I have spent 20 days and the program is still running. I am not sure if the program is running properly. I have added parallel to the environment variables

[YouxinZhao]

the Genome size is 2.6Gb. The hic data is 400Gb

[Nabs2000]

Hi, did you manage to speed things up? I am running the juicer.sh pipeline using the chm13 reference (2.2 GB) and paired end reads (4 pairs of gzip files -> 129GB in total), and the process is very slow for me too.