Racon consumes too much memory

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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Racon consumes too much memory #167

Open TypicalSEE opened 4 years ago

TypicalSEE commented 4 years ago

Hi, I am using Racon to polish a small plant genome(~ 300Mb). But I noticed that Racon consumes about 250GB memory, which seems to be a little high. The PAF file generated by minimap2 is of 1.9GB size and the ONT gzipped fastq file is ~50GB. Is there any way to reduce the memory usage? Thanks!

rvaser commented 4 years ago

Hello, Racon loads all the input files into memory, hence the high memory consumption. You could try using the racon_wrapper to downsample the reads, but that might affect accuracy.

Best regards, Robert