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muTect ressources

Hi all,
I am using muTect on whole genome data and I am wondering the computing ressources it needs.
When I launch it on my data it starts well and after a couple of hours it stops writing result and just freeze.
I run each chromosome separately and I give 8 threads each time. The machine CPU is full but nothing is written out anymore.

Before I was using the beta test version of muTect and there was no problem. What do you think can explain this?
Does the new version need more ressources?

Thanks for your help


  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    Hi -- that's very puzzling as many users analyze WGS data on a regular basis. When we run WGS data we typically divide the genome into 100 equally sized chunks (rather than by chromosome) and run them independently using a single thread. Could you try something like that (not multi-threaded) and let me know how it works as a way to narrow down the problem?


  • ltononltonon Member

    Hi, I did what you suggested and it worked well. The different chunks run with a single thread and it takes between 1 and 2 hours for muTect to process them. So I think the problem is with the mutlithreading right?
    I also noticed that the walker spent less time in waiting for I/O when i do not use the multithreading. Does it help to understand what is going on?

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