DADA2 in QIIME2 - Return Code 1

I am pretty new to using QIIME2. I have already imported my data via the manifests version, and I am currently trying to denoise my data using DADA2. I keep getting Return Code one, and I did to a ‘qiime tools validate’ on the file and everything seems to be ok. Not sure how to proceed. Also, I did run a q-score on the data as well and everything seems to be ok. My error is pasted below. Thanks!

qiime dada2 denoise-paired \

–i-demultiplexed-seqs paired-end-demux.qza
–p-trim-left-f 15
–p-trim-left-r 15
–p-trunc-len-f 225
–p-trunc-len-r 205
–p-n-threads 0
–o-table table.qza
–o-representative-sequences rep_seqs.qza
–o-denoising-stats denoising_stats.qza
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/tmp450ej6il/forward /tmp/tmp450ej6il/reverse /tmp/tmp450ej6il/output.tsv.biom /tmp/tmp450ej6il/track.tsv /tmp/tmp450ej6il/filt_f /tmp/tmp450ej6il/filt_r 225 205 15 15 2.0 2.0 2 consensus 1.0 0 1000000

R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4

  1. Filtering Error in names(answer) <- names1 : attempt to set an attribute on NULL
    Execution halted
    Traceback (most recent call last):
    File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/”, line 257, in denoise_paired
    File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/”, line 36, in run_commands, check=True)
    File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/”, line 418, in run
    output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmp450ej6il/forward’, ‘/tmp/tmp450ej6il/reverse’, ‘/tmp/tmp450ej6il/output.tsv.biom’, ‘/tmp/tmp450ej6il/track.tsv’, ‘/tmp/tmp450ej6il/filt_f’, ‘/tmp/tmp450ej6il/filt_r’, ‘225’, ‘205’, ‘15’, ‘15’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘0’, ‘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/qiime2-2019.10/lib/python3.6/site-packages/q2cli/”, line 328, in call
results = action(**arguments)
File “</home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/>”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/”, line 240, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2019.10/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.

Plugin error from dada2:

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

See above for debug info.

I encountered this error when I hadn’t enough of memory for the analysis. Maybe you just don’t have enough of RAM

1 Like


Thank you for the response. I have 8GB of RAM on my Windows computer; however, I’m using Virtural Box to run QIIME2. Also, I changed the number of cores to 2 using the p-n-threads command. Knowing this, would this still produce the same error?

Yes, it can be. 16 or 32 gb would be nice

Welcome to the forum @KCalapa!

You should allocate as much memory to the VM as possible (see the VB manual for instructions)

Good luck!

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