Dada2 error running

Hi all. A newbie in bioinformatic field here. I am facing a problem when I was trying to run Dada2 with my samples. I received error code below and i dont understand what it means:

(qiime2-2019.7) [email protected]:~/Desktop$ qiime dada2 denoise-single --i-demultiplexed-seqs single-end-reads.qza --p-trunc-len 300 --p-trim-left 0 --p-n-reads-learn 500 --output-dir dada-output --verbose > dada-stats
Loading required package: Rcpp
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/”, line 154, in _denoise_single
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/”, line 36, in run_commands, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-byceh899/7408ed00-290c-4026-aa01-4f9bcf0fd52a/data’, ‘/tmp/tmpopeoln55/output.tsv.biom’, ‘/tmp/tmpopeoln55/track.tsv’, ‘/tmp/tmpopeoln55’, ‘300’, ‘0’, ‘2.0’, ‘2’, ‘Inf’, ‘consensus’, ‘1.0’, ‘1’, ‘500’, ‘NULL’, ‘16’]’ died with <Signals.SIGKILL: 9>.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/”, line 327, in call
results = action(**arguments)
File “</home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/>”, line 2, in denoise_single
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/”, line 240, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/”, line 189, in denoise_single
File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/”, line 165, in _denoise_single
" 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.

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.

My samples are 16s rDNA extracted from plant.
I really need to know which steps gone wrong.
Thank you.

Welcome to the Qiime 2 forums! :qiime2:

Let’s see if I can help answer your question.

Thanks for posting your full command and error code. That’s really helpful. :+1:

As you have identified, you got a -9 error when running dada2. The -9 error means that the process was ‘killed’ or canceled by something on the linux system.

A job could be canceled because it was running too long, or using too much RAM / memory, or was canceled by another user.

Can you tell me more about the computer you are using to run Qiime 2? Is it a laptop or a server / supercomputer? :computer: :desktop_computer:
How much RAM / memory does your computer have, and how large is your single-end-reads.qza file?


P.S. I noticed this:

--p-n-reads-learn 500

That’s a great number of reads to use for testing, but when you are ready to analysis data for publication, make that number bigger!