Dada2 Fails: Error Log Attached

Technical Support
1

Hello,

I am on an M2 macbook pro running qiime2 2023.5 in a docker container. I followed the installation process detailed in the qiime2 docs for the docker install. Qiime2 loads and works! However, in the moving pictures tutorial the following command fails:

qiime dada2 denoise-single \
  --i-demultiplexed-seqs demux.qza \
  --p-trim-left 0 \
  --p-trunc-len 120 \
  --p-n-threads 12 \
  --o-representative-sequences rep-seqs-dada2.qza \
  --o-table table-dada2.qza \
  --o-denoising-stats stats-dada2.qza

The output is:

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Debug info has been saved to /tmp/qiime2-q2cli-err-7b5l16sn.log

Attached is the log output. I feel like this is an issue due to being on apple silicon, however, I activated the docker environment specifying linux/amd64.

This is how I start my docker qiime2 container.

docker run --platform linux/amd64 --rm -it \
    -u $(id -u):$(id -g) \
    -v $(pwd):/data \
      quay.io/qiime2/core:2023.5 \
        /bin/bash

Thanks in advance for your insight!

Stephan
qiime2-q2cli-err-nezves5p.txt (4.1 KB)

2

Hi.
It is performance problem. See Denoising error, names attribute must be the same length as vector - #2 by Nicholas_Bokulich
Regards, SN

3

Thanks SN,

Oh yes, thats true for me too. It worked with 1 core but took quite a while and used less than 10% of the cpu.

This seems like a bug to me. Are there any plans for fixing it? Dada2 should at least say how many cores can work based on the data size or output an error message that says something like: "too many cores used".

Best,

Stephan

4

Nice!

You can ask for it directly here GitHub - benjjneb/dada2: Accurate sample inference from amplicon data with single nucleotide resolution

Regards,
SN

5

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