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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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predicting peak memory of a large run #159

Open PeterEmmrich opened 4 years ago

PeterEmmrich commented 4 years ago

Hi Ivan! I am trying to polish a 6.2 Gbp assembly using racon 1.3.1. I would like to feed it 301 Gb of Fastq long reads (PromethION) and a 15 Gb PAF file (without CIGAR).

I tried this with 32 cores and 200G memory, but it crashed due to memory capping out after about two days.

I can request more memory, but I would like to get it right. Could you advise on how much memory usage and wall-clock time you'd expect this to take and how many cores I should use?

Many thanks and I hope you are staying safe. Peter

rvaser commented 4 years ago

Hi Peter, the memory is bound by the cumulative size of all three files needed as input plus some epsilon. For your case, I would say that 500Gb of RAM should be more than enough. Regarding the execution time, not sure how long it will take :/

Best regards, Robert

P.S. I would advise you to upgrade to the latest Racon version (1.4.12) at https://github.com/lbcb-sci/racon.