Hello everyone.
As a "side dish" of my main mission, I have to run juicer, the Hi-C tool from aiden lab, to assess the ressources it would need on our cluster. I am therefore using the bash wrapper for Slurm called myJuicer.sh, which manage the different jobs to be submitted with the proper memory and thread options.
The script is quiet complicated for me to read and I struggle to understand which thread starts when and depends on whom etc. And there are so many of them ! I would need help to understand exactly what every of them is doing. So far, this is what I deducted from observing my jobs being submitted :
I am pretty confident in my understanding of the split, align and merge steps, and I also know the order they chain to each others... But for the others steps (is my list of thread even complete or some job go to fast to be seen ?), I'm not really sure of what they are doing and who comes first.
I think check verify files integrity, HIC30 and HIC should be the thread to calculate Hi-C stats (but I just discovered there is also a "stats" thread). I have no idea for fragm, post, dedup, prep, arrow, hicup ...
Also often, some jobs are in the state "JobHeldUser" and may have to be killed in order to unlock the others jobs. But I don't quite understand if this is normal or not...
Any Hi-C veteran could explain to me those others steps purpose and how they chain together ?
Thanks you for your help !
Roxane
