How many cores does deblur or dada2 use?

How many cores does deblur or dada2 use? I know some plugins can use more than one core, so I wanted to see how much these used so I can optimize my processing. Furthermore, the more cores I ask my supercomputer center for, the longer it takes for them to actually start the processing, so I want to ask for the most it can use but no more. Thanks!

Hello Mike,

Both deblur and dada2 are pretty efficient, so they will use as many cores as you can give them!
(Well, as many cores on a single node!)

You could ask your supercomputer center how many cores/threads are on one node, then pass that to dada2 and deblur.

Some supercomputer centers have a ‘short queue’ especially for programs like deblur and dada2 that only run on a single node. This short queue is often very fast to start processing, so it’s a perfect fit for your programs.

Colin

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Thanks,

What about the plugin demux?

Take a look at the Methods section for the plugin.
https://docs.qiime2.org/2019.7/plugins/available/demux/

If you see a --p-cores or --p-threads option, then it can use multiple cores. If not, just one core is used.

Let me know what you conclude!
Colin

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They don’t seem to be there, so I’ll assume 1 then. Thanks!
Link: https://docs.qiime2.org/2019.7/plugins/available/deblur/denoise-16S/

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deblur denoise-16S supports multiple jobs via the --p-jobs-to-start flag.

What do you mean jobs? Multiple denoising if I had multiple files to denoise?

Not sure (I am just quoting the plugin doc), you’ll have to check the deblur docs to check their definition of “jobs” out:

Deblur can operate in parallel. The number of threads can be specified by the -O NNN flag (default it 1). Running more threads than available cores is not advised.

Looks like “jobs” means “threads” here.

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