Problem with DADA2


I am trying to use the dada2 denoise-paired command on version 2017.8 but I keep experiencing the same error. The code I'm using is:

qiime dada2 denoise-paired \
   --i-demultiplexed-seqs ~/data/djcabral/qiime2_test/demux.qza \
   --o-table ~/data/djcabral/qiime2_test/table.qza \
   --o-representative-sequences ~/data/djcabral/qiime2_test/rep-seqs.qza \
   --p-trim-left-f 20 \
   --p-trim-left-r 20 \
   --p-trunc-len-f 240 \
   --p-trunc-len-r 180 \
   --p-n-threads 0

The command will run for a while (usually over an hour) before giving me the following error:

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 /users/djcabral/data/djcabral/qiime2_test/qiime2-q2cli-err-8is8dwp6.log

I have attached the log file that is generated. It appears that the error occurs during chimera detection but I can't quite figure out the issue or how to fix it. Does anyone have any ideas or suggestions? Thanks in advance!
error.txt (248 Bytes)
qiime2-q2cli-err-8is8dwp6.txt (7.2 KB)

Thanks for the detailed post @djcabral92! I was peeking through qiime2-q2cli-err-8is8dwp6.txt and it looks like you somehow have an older version of dada2 in your conda environment (1.2.0), but q2-dada2 should be using 1.4.0.

I suspect this is because you have an installation of R outside of your QIIME 2 environment. Please take a look at this post and see if the directions linked to there fix the problem for you. If not, please provide the output from the following commands, after activating your QIIME 2 environment:

  1. $ conda list
  2. $ which R

Thanks! :t_rex:

1 Like

Thanks for the quick response! You were right - I did have old version of R that I no longer use installed outside of my QIIME2 environment . I uninstalled the old version of R (along with the dada2-1.2.0 package) and it fixed the problem without having to add a .Rprofile file. Thanks for the help!


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