I have been having this problem for more than a week now and I am running out of time and patience.This problem occurs when I run my script on a Mac and when I run it on a PC (no difference of results from more RAM, it just aborts faster). When I try to run this line of my dataset, the session aborts.
set.seed(119)
tax_PR2 <- assignTaxonomy(seqtab,
"~/Desktop/Documents/Bruts/aeDNA_data_shared/pr2_version_4.11.1_dada2.fasta",
multithread=TRUE)
Does anyone have any idea of what the problem is? I verified my dataset (seqtab is currently considered by R as a large matrix of 3930724 elements of 20.2Mb), I verified the space I have on my computer, I have all the needed packages to run this line of code and I tried different sources of genome database for PR2 (PR2 version 4.11.1 or 4.12.0 etc...) and it always has the same result.
If you have any ideas I would appreciate them. I hope the information I gave is sufficient.
Packages installed:
library(BiocManager)
library(Rcpp)
library(dada2)
library(ff)
library(ggplot)
library(gridExtra)
library(phyloseq)
library(vegan)
This is probably caused by a bug that was introduced in 1.14, see the Github issue here for more information: https://github.com/benjjneb/dada2/issues/916
We've just identified the cause, and a fix should be out soon. For immediate use, the workaround is to turn off multithreading, or to revert to the previous release 1.12.