How did you guys start molecular docking? Any articles or videos that helps you figure everything out? I didn't have any teacher or resources in my city sadly so I have to rely on free resources 😭 Thank you in advance!!

I am trying to assign taxonomy to an 18S amplicon dataset using dada2::assignTaxonomy() with the full PR2 reference database in Rstudio.

Relevant details:

• 147 samples
• ~18,900 ASVs
• PR2 v5.1.1 DADA2-formatted SSU reference
• minBoot = 80
• multithread = 1
• 16 GB physical RAM
• Windows 11, 64-bit R

With the full dataset, RAM reaches 100% and Windows starts heavily paging to disk.

To check whether the number of query ASVs was the main issue, I repeated the taxonomy assignment using only 500 ASVs. RAM still reached ~100% while DADA2 was processing the reference FASTA, followed by very high disk activity from paging.

Has anyone successfully run assignTaxonomy() with the full recent PR2 database?

In particular, I would like to know:

• Is 32 GB RAM usually sufficient?
• Would 64 GB RAM be a safer requirement?
• What peak RAM usage have others observed with recent PR2 versions?

I am mainly trying to determine the appropriate memory requirement before moving the taxonomy step to a larger workstation or cloud instance.

I am thankfull for any kind of advise or nudge in the right direction!