How long does assigntTaxonomoy takes with UNITE database?

[sadia-marjia]

My issue is same as #1808 . I'm running on a 16GB RAM computer. My DADA2 package version is 1.32.

I've been following DADA2 ITS workflow and have gotten to the part where I get to assign taxonomies. The command was

unite.ref <- "/Users/sadiamarjia/Library/CloudStorage/Box-Box/Hegarty\ Lab/ResearchAreas/A\ walk\ in\ the\ park/Ref_Database/sh_general_release_s_04.04.2024/sh_general_release_dynamic_s_04.04.2024.fasta"

taxa_ITS <- assignTaxonomy(seqtab_ITS.nochim, unite.ref, multithread = TRUE, tryRC = TRUE)

It is running for a more than 2 hours. I want to know how long does it take to be complete on average?

[benjjneb]

It depends on how many sequences you are trying to classify. And whether you have enough memory to fit the database itself into memory comfortably.

I would try testing with a small number of sequences, like 100, to start. Then you can time a few larger sets of sequence and extrapolate out to how long it will take for your full dataset.