qiime2 2021.4 dada2: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

[tyz]

Hi, thanks for seeing this. I’m using qiime2-2021.4 in Linux. I run dada2 with this command:
time qiime dada2 denoise-paired
--i-demultiplexed-seqs demux.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 190
--p-trunc-len-r 220
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
I got this error:
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
The log file:
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/tmpklgag9c0/forward /tmp/tmpklgag9c0/reverse /tmp/tmpklgag9c0/output.tsv.biom /tmp/tmpklgag9c0/track.tsv /tmp/tmpklgag9c0/filt_f /tmp/tmpklgag9c0/filt_r 190 220 0 0 2.0 2.0 2 12 independent consensus 1.0 1 1000000

R version 4.0.3 (2020-10-10)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.6 / RcppParallel: 5.1.2

1. Filtering ..........
2. Learning Error Rates
   242892960 total bases in 1278384 reads from 4 samples will be used for learning the error rates.
   Error in dada_uniques(names(drpi$uniques), unname(drpi$uniques), names(drpi$uniques) %in% :
   Memory allocation failed.
   Execution halted
   Warning message:
   system call failed: Cannot allocate memory
   Traceback (most recent call last):
   File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 266, in denoise_paired
   run_commands([cmd])
   File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
   subprocess.run(cmd, check=True)
   File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/subprocess.py", line 516, in run
   raise CalledProcessError(retcode, process.args,
   subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpklgag9c0/forward', '/tmp/tmpklgag9c0/reverse', '/tmp/tmpklgag9c0/output.tsv.biom', '/tmp/tmpklgag9c0/track.tsv', '/tmp/tmpklgag9c0/filt_f', '/tmp/tmpklgag9c0/filt_r', '190', '220', '0', '0', '2.0', '2.0', '2', '12', 'independent', 'consensus', '1.0', '1', '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/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 279, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

I don’t know why this happened. I did some attempts and did not find a suitable solution.
Can anyone help me?
Thanks a lot!

[ChrisKeefe]

Welcome to the forum, @tyz! This is probably an out of memory issue, which you can correct by allocating more memory (if on a cluster or VM), or by working on a system with more available RAM. Try searching this forum for "DADA2 system call failed: Cannot allocate memory", read a few of the posts you find, and let me know if you need further help.

[tyz]

It's really a memory problem,Your answer helped me a lot. Thank you very much.