Errno 2: no such file or directory: run_dada_single.R

Hi all,

I am having trouble with running dada2 denoise-single. The error I am getting is errno 2 no such file or directory: run_dada_single.R does this mean there’s something wrong with my installation? Please see the debug log

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Good morning @Palesa,

Thanks for posting your traceback! Would you be willing to post the command you ran as well?

The file run_dada_single.R should be included with Qiime 2… but it looks like you are running qiime2-2018.6, while the current version is qiime2-2019.7. In general, the newest versions of Qiime will have more features so and better support, so it might be worth updating to the newest version of Qiime.

Let me know what you find!


hi Colin,

here is the command:
/Users/blaqunicorn/miniconda3/envs/qiime2-2018.6/bin/qiime dada2 denoise-single --i-demultiplexed-seqs SRRfastq/demux_474390.qza --p-trim-left 0 --p-trunc-len 430 --p-trunc-q 10 --o-representative-sequences rep-seqs-dada2_474390.qza --o-table SRRfastq/table_dada2_474390.qza --o-denoising-stats SRRfastq/stats_dada2_474390.qza

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That command looks OK to me. I’m not sure why it wouldn’t work. Let’s see what one of the Qiime devs recommend.

It might still be advantageous to install the newest version of Qiime. And don’t worry, you can install the newest version into a new conda environment, without messing up your current install of qiime2-2018.6!

ok, yeah I have been worried that if I update its will mess up my current installation. now that I know that it won’t, let me update. thank you. will let you know if the error persists with the latest version.

thank you Colin.


It looks like the 2018.6 installation already is messed up - this file should be included in your deployment. I agree with @colinbrislawn’s suggestion - please upgrade to a newer version of QIIME 2. In the meantime though, I am curious to see the results of the following command when run in your activated 2018.6 environment:

# first, activate your 2018.6 env, then:
ls $CONDA_PREFIX/bin/*.R

This should show a listing of R scripts in your conda environment for 2018.6.


Hi @Palesa and all,

small thing I’ve noted from the picture you sent, it looks like you activated the ‘base’ conda environment, so that you have to specify the full path for the qiime plug in in the command.

That of course if my interpretation of the picture is correct!

Could you try:
conda deactivate
source activate qiime2-2018.6

Then retry your qiime2 script?


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