return code -9 error encountered while running DADA2 in R

[Giulia_Gionchetta]

Dear Colleagues
I am using QIIME2 2019.10.0 on Ubuntu 18 for amplicon analysis. DADA2 is giving some errors.

Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-pinunehm.log

This is the log error given.

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/tmpm4ecjxao/forward /tmp/tmpm4ecjxao/reverse /tmp/tmpm4ecjxao/output.tsv.biom /tmp/tmpm4ecjxao/track.tsv /tmp/tmpm4ecjxao/filt_f /tmp/tmpm4ecjxao/filt_r 200 200 20 20 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 Traceback (most recent call last):
   File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 257, in denoise_paired
   run_commands([cmd])
   File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
   subprocess.run(cmd, check=True)
   File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
   output=stdout, stderr=stderr)
   subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpm4ecjxao/forward’, ‘/tmp/tmpm4ecjxao/reverse’, ‘/tmp/tmpm4ecjxao/output.tsv.biom’, ‘/tmp/tmpm4ecjxao/track.tsv’, ‘/tmp/tmpm4ecjxao/filt_f’, ‘/tmp/tmpm4ecjxao/filt_r’, ‘200’, ‘200’, ‘20’, ‘20’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘0’, ‘1000000’]’ died with <Signals.SIGKILL: 9>.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, 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/_denoise.py”, line 272, 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.

This is my command.
qiime dada2 denoise-paired --i-demultiplexed-seqs network-first-demux.qza --p-trim-left-f 20 --p-trim-left-r 20 --p-trunc-len-f 200 --p-trunc-len-r 200 --p-n-threads 1 --o-table netw_asvtable.qza --o-representative-sequences netw_rep_seqs.qza --o-denoising-stats netw_denoising_stats.qza

[ChrisKeefe]

Welcome to the forum, @Giulia_Gionchetta!
These SIGKILL errors are often out-of-memory errors, caused by your system being under-resourced. Are you running QIIME 2 on a virtual machine? A cluster? A personal machine with QIIME 2 installed natively? If not the latter, how much RAM have you allocated for the program?

Thanks,
Chris

[Giulia_Gionchetta]

Thank you @ChrisKeefe I have already solved the problem allocating more CPUs in the qiime2 virtual machine.
thank you!
Giulia