DADA2 denoise-paired error: R (return code -9)

User Support
1

I am running QIIME2 2017.9 in a Virtual Box, and I ran the following command:

qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-paired-end.qza
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 200
–p-trunc-len-r 200
–o-table table.qza
–o-representative-sequences rep-seqs.qza

And received this error:

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

I was looking at the forum, but most of things are about code 1, even -11.

I don’t know how to interpret this error. Any idea?

Thanks!

2

Hi, I think that you are running out of memory, how strong is your machine? If not very strong, you can try perform quality filtering first to get read of excessive reads

3

Hi!!
It has 8 Mb of RAM, but I’m not sure how much takes Virtual Box to run Qiime2. I think this details cann’t be change once Qiime2 package has been loaded on VB.
Do you know how much memory is necessary to use Qiime2?

5

8 gb, I suppose, not 8 mb =). I don’t know exactly but once I took a look in htop during DADA2 and it was taking about 7 gb of RAM. You can filter your data to decrease the ammount of processes or try use half of the number of your threads using
–p-n-threads

6

Hey there @YisBel!

You should be able to change the allocation - please check out virtualbox.org for links to their docs/support forum/etc (we do not develop Virtualbox).

There is no single answer to this, since every dataset and analysis of it is totally unique. As far as DADA2 goes, please see the following:

https://benjjneb.github.io/dada2/bigdata.html#how-long-does-it-take

8

thanks!!

This information was very useful

9

thaks, I wil try to filter my data like you said. I figured out how increase memory to VB also.

10

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