Qiime 2 decontam

R crashes whenever I run this line of code --> table(contamdf.prev$contaminant)

library(phyloseq); packageVersion("phyloseq")

Now time to actually move through the tutorial in the prevalence section. Here we start with default threshold = 0.1

sample_data(physeq)$is.neg <- sample_data(physeq)$type == "negative-control"
contamdf.prev <- isContaminant(physeq, method="prevalence", neg="is.neg")
write.table(contamdf.prev, file = "decomtam0.1.txt", sep = "\t", quote = FALSE, row.names = T)

You are not giving us much information to debug, but you are likely running out of RAM. Have in mind that PositCloud's free plan is caped to 1GB of RAM

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