Error when running DADA2

[Zimtblatt]

Dear all,

after working with QIIME2 on two datasets, I started working on a third dataset and become the following error code every time I am trying to run dada2:

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-kqyydc47.log

I am working in the virtual machine on windows 10.

thank you very much for your help!

Isabelle

[Nicholas_Bokulich]

Hi @Zimtblatt,

@Zimtblatt

running DADA2 in R (return code -9)

This is a memory error. See here for support with this error on virtualbox:

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

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 abo…

Good luck!

[Zimtblatt]

Hi Nicholas,

thank you very much for the rapid reply!

I am a bit confused now. In the link you provided they recommend quality filtering before starting dada 2. Yet, I can find other posts, where quality filtering prior to DADA2 is not recommended:
DADA2 and quality filtering?

In another post they provide a linke to the DADA2 homepage where they suggest a stepwise approach for big datasets. A DADA2 workflow for Big Data (1.4 or later)
How can I do this in QIIME.

thank you so much for your help!!

kind regards,

Isabelle

[Nicholas_Bokulich]

Hi @Zimtblatt,

The dada2 workflow in QIIME 2 performs quality filtering as an initial step so earlier filtering is unnecessary. It probably would not hurt, but would be redundant. Hence the mixed messages in different forum posts.

@Zimtblatt

In another post they provide a linke to the DADA2 homepage where they suggest a stepwise approach for big datasets. A DADA2 workflow for Big Data (1.4 or later)
How can I do this in QIIME.

That link seems to describe the dada2 workflow that is already implemented in QIIME 2.

return code -9 is a memory error — the best fix is to find a more powerful machine to run this on.

Good luck!

[Zimtblatt]

Dear Nicholas,

thank you very much for the instant reply!

Yes, I understood that QIIME2 performs quality filtering step. So you think filtering would not help with the memory problem? Unfortunately I do not have access to a more powerful computer.
Should I change the settings for the virtual machine while running DADA2?

Any ideas how I could solve the problem without a more powerful computer?

thank you so much!

Isabelle

[Nicholas_Bokulich]

@Zimtblatt

Should I change the settings for the virtual machine while running DADA2?

Yes, give your virtual machine more memory if you can. Wow, 2048 MB is not much... you will probably need at least 4 GB RAM for an average dada2 run (that is a very rough guess). Let us know if that helps!