dada2 denoise-paired error(return code 1)

I have question about dada2 denoise-paired error(return code 1).

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada_paired.R /tmp/tmp3pqbe1yz/forward /tmp/tmp3pqbe1yz/reverse /tmp/tmp3pqbe1yz/output.tsv.biom /tmp/tmp3pqbe1yz/track.tsv /tmp/tmp3pqbe1yz/filt_f /tmp/tmp3pqbe1yz/filt_r 200 200 0 0 2.0 2.0 2 consensus 1.0 24 1000000

R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.3 / RcppParallel: 4.4.4

  1. Filtering Error in names(answer) <- names1 :
    'names' attribute [63] must be the same length as the vector [12]
    Execution halted
    Traceback (most recent call last):
    File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/", line 257, in denoise_paired
    File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/", line 36, in run_commands, check=True)
    File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/", line 418, in run
    output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp3pqbe1yz/forward', '/tmp/tmp3pqbe1yz/reverse', '/tmp/tmp3pqbe1yz/output.tsv.biom', '/tmp/tmp3pqbe1yz/track.tsv', '/tmp/tmp3pqbe1yz/filt_f', '/tmp/tmp3pqbe1yz/filt_r', '200', '200', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '24', '1000000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/", line 328, in call
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/>", line 2, in denoise_paired
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/", line 245, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/", line 272, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Could you please assist?
Thank you!


This part of the error message jumps out at me:

We usually see that error pop up from within DADA2 when you utilize too many threads on your host machine. Set --p-n-threads down to a lower number and try again.


1 Like

Thank you.
I solve problem, just like you said to me.
I was wrote --p-n-treads 1.(12, 6, 4 were not working!!)
–p-n-treads 1 was need a long time.

So, i have another question!
my computer ram is 8G, it is enough to use qiime2 program?

1 Like

Glad to hear you resolved it!

8 GB is very low (that is barely enough to run Microsoft Office today, or the Google Chrome browser), but, if you were able to get through DADA2, you should be fine. You will certainly not be able to train your own feature classifier, so you will need to look at using a pre-trained classifier, instead (link). Feel free to open a new Topic if you have additional questions. Thanks!


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