How much RAM is needed for feature classification?

[Nicholas_Bokulich]

Hi @ctekellogg,

@ctekellogg

Is there a way to figure out how much RAM the Naive Bayes classifier would need to classify a 20 MB OTU/rep set fasta file?

No, there is not really a straightforward way to estimate, but I can offer a few tips to lower memory consumption.

1. The main factor driving memory use is the size of the reference sequence database. So using smaller reference sequence databases (e.g., greengenes rather than SILVA) and shorter sequences will reduce memory load.
2. See this post for some other tips (chunk-size is now called reads-per-batch)

@ctekellogg

Similarly, how much RAM would be necessary for deblur or DADA2 to process a 25-30 GB fastq file?

@benjjneb and @wasade may be able to offer some advice on memory consumption with these methods.

I hope that helps!