removeBimeraDenovo freezing then crashing

[damianasrojas]

I am a novice at microbiome data analysis and am running the DADA2 pipeline for the first time.

When I try to run seqtab.nochim <- removeBimeraDenovo(seqtab, method="consensus", multithread=TRUE, verbose=FALSE) R becomes non responsive then crashes.

Here is the information you have requested in previous problems, I am also running this on a super computer with 4 cores and 32GB of data.

packageVersion("dada2")
[1] ‘1.26.0’
dim(seqtab)
[1] 27 143442
summary(nchar(getSequences(seqtab)))
Min. 1st Qu. Median Mean 3rd Qu. Max.
260 292 292 292 292 352

[damianasrojas]

Additionally, I have tried setting both multithreading and verbose to false and it still does not work.

[benjjneb]

Those diagnostics all look normal and like things should run.

Can you try running removeBimeraDenovo on subsets of the data -- is there a dataset size at which this crash manifests? Or does it happen at any dataset size?

To try on the first X ASVs:

XX <- 100
seqtab_sub <- seqtab[,1:XX]

Then run your removeBimeraDenovo(...) command on seqtab_sub.