Dada2 error (return code -9)

I ran the following dada2 command on demultiplexed paired-end data that were imported using a Phred 33 manifest file.Uploading…

qiime dada2 denoise-paired
–i-demultiplexed-seqs paired-end-demux.qza
–p-trunc-len-f 200
–p-trunc-len-r 180
–p-trim-left-f 0
–p-trim-left-r 0
–o-table table-dada2.qza
–o-representative-sequences rep-seqs-dada2.qza

I get the following error:

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/tmpl_fzwx9c/forward /tmp/tmpl_fzwx9c/reverse /tmp/tmpl_fzwx9c/output.tsv.biom /tmp/tmpl_fzwx9c/filt_f /tmp/tmpl_fzwx9c/filt_r 200 180 0 0 2.0 2 consensus 1.0 1 1000000

R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0

  1. Filtering .
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    Traceback (most recent call last):
    File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/”, line 179, in denoise_paired
    File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/”, line 35, in run_commands, check=True)
    File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/”, line 398, in run
    output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpl_fzwx9c/forward’, ‘/tmp/tmpl_fzwx9c/reverse’, ‘/tmp/tmpl_fzwx9c/output.tsv.biom’, ‘/tmp/tmpl_fzwx9c/filt_f’, ‘/tmp/tmpl_fzwx9c/filt_r’, ‘200’, ‘180’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status -9

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/”, line 224, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/”, line 228, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/”, line 194, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.

I’m not sure how to proceed. Thanks for your help!

Hi @Erin_Eggleston! The -9 exit code from DADA2 usually means that your system is running out of memory (RAM). Can you try increasing the amount of available memory and then rerun the command?

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