DADA2 error message code -9


I was running dada2 with my 23 million reads of data(212 samples).
I entered codes like this;

qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trunc-len-r 280 --p-trunc-len-f 280 --o-table table-dada2.qza --o-representative-sequences rep-seq-dada2.qza --o-denoising-stats stats-dada2.qza

However, while running this step, a message was displayed on my monitor;

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.

Debug info has been saved to /tmp/qiime2-q2cli-err-vrk0nyiz.log

Is there anyone who experienced same situation and how did you solve this problem.

Thank you for reading this message.


Hi @Jeong,

Searching for “DADA2 -9” on the forum should yield a lot of results. This exit code 99.9% of the time means that your process was killed. This can be because you are using a scheduler and hit walltime limits, or more commonly your ran out of memory in a virtual-box situation. In any case, something killed your process (be that you, a scheduler, or the operating system itself).

Hope that helps!


Thanks for the reply.
My virtual box’s RAM was 1GB.
I’ve changed it to 7109MB and it works well now, but I wonder that is it the adequate memory?

Hi @Jeong,

Yes that should be enough for most things in QIIME 2 except for training some classifiers, but we have pre-trained ones available since that’s a pretty common problem to have :slight_smile:

Thank you so much. Finally I finished DADA2 with my 28million reads of 212samples within 48hours with my Macbook pro(double core, 8GB RAM).
Now I can predict running time roughly with my macbook.
(Unfortunately I couldn’t finished analysis with my ubuntu, because the analysis with macbook was finished earlier.)

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