An error was encountered while running DADA2 in R (return code -9)

[JordanS (Jordan)]

Hi,

Sorry in advance if this seems like a silly question- new to qiime 2.
I am currently running the following command:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-paired-end.qza
–p-trim-left-f 5
–p-trim-left-r 5
–p-trunc-len-f 125
–p-trunc-len-r 124
–o-table table
–o-representative-sequences rep_seqs
–o-denoising-stats denoising_stats

I ended up getting an error: Plugin error from dada2: Error in 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. I looked into the file, and it gave me the information below:

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 /short/dq69/js1541/tmp/tmpymauwf7q/forward /short/dq69/js1541/tmp/tmpymauwf7q/reverse /short/dq69/js1541/tmp/tmpymauwf7q/output.tsv.biom /short/dq69/js1541/tmp/tmpymauwf7q/track.tsv /short/dq69/js1541/tmp/tmpymauwf7q/filt_f /short/dq69/js1541/tmp/tmpymauwf7q/filt_r 125 124 5 5 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 Traceback (most recent call last):
   File “/short/dq69/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
   run_commands([cmd])
   File “/short/dq69/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
   subprocess.run(cmd, check=True)
   File “/short/dq69/miniconda3/envs/qiime2-2018.11/lib/python3.5/subprocess.py”, line 398, in run
   output=stdout, stderr=stderr)
   subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/short/dq69/js1541/tmp/tmpymauwf7q/forward’, ‘/short/dq69/js1541/tmp/tmpymauwf7q/reverse’, ‘/short/dq69/js1541/tmp/tmpymauwf7q/output.tsv.biom’, ‘/short/dq69/js1541/tmp/tmpymauwf7q/track.tsv’, ‘/short/dq69/js1541/tmp/tmpymauwf7q/filt_f’, ‘/short/dq69/js1541/tmp/tmpymauwf7q/filt_r’, ‘125’, ‘124’, ‘5’, ‘5’, ‘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 “/short/dq69/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/short/dq69/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/short/dq69/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/short/dq69/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 246, 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 am unsure why this has happened?

Any help is appreciated!

Thanks in advanced,
Jordan

[Nicholas_Bokulich]

Hi @JordanS,
Not a silly question, but a very common one on the forum

Return code -9 is a memory error and you will need a more powerful machine to run — see the search results linked above to see more troubleshooting advice.

Good luck!