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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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GPU nodes #299

Closed ghost closed 2 years ago

ghost commented 2 years ago

Hi,

I am trying to run Megalodon with 1 GPU node, but it is not able to identify the GPU node, how can I do it? Also, it is possible to obtain more information about the speed and time it takes to analyse for example 1GB of data?

Thank you in advance !

marcus1487 commented 2 years ago

The --devices 0 value should specify to use the cuda:0 device on your machine. The default is CPU only computation. There are far too many systems and settings within megalodon to provide sufficient computational benchmarks. Please see the production Guppy basecaller benchmarks for this purpose.