dada2 error (return code1)

Below are the error codes:
$ qiime dada2 denoise-paired --i-demultiplexed-seqs demux_clean.qza --p-trunc-len-f 237 --p-trunc-len-r 179 --p-trim-left-f 0 --p-trim-left-r 14 --p-n-threads 2 --output-dir dada2_clean.out --o-representative-sequences repseqsC1_clean.qza --o-table tableC1_clean.qza --o-denoising-stats denoise-statsC1.qza --verbose
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 /scratch/lngor001/tmpxas0pfum/forward /scratch/lngor001/tmpxas0pfum/reverse /scratch/lngor001/tmpxas0pfum/output.tsv.biom /scratch/lngor001/tmpxas0pfum/track.tsv /scratch/lngor001/tmpxas0pfum/filt_f /scratch/lngor001/tmpxas0pfum/filt_r 237 179 0 14 2.0 2.0 2 12 independent consensus 1.0 2 1000000

R version 4.1.2 (2021-11-01)
Loading required package: Rcpp
DADA2: 1.22.0 / Rcpp: / RcppParallel: 5.1.5

  1. Filtering Error in names(answer) <- names1 : attempt to set an attribute on NULL
    Execution halted
    Traceback (most recent call last):
    File "/opt/linux/rocky/8.x/x86_64/pkgs/qiime2/2022.2/lib/python3.8/site-packages/q2_dada2/", line 279, in denoise_paired
    File "/opt/linux/rocky/8.x/x86_64/pkgs/qiime2/2022.2/lib/python3.8/site-packages/q2_dada2/", line 36, in run_commands, check=True)
    File "/opt/linux/rocky/8.x/x86_64/pkgs/qiime2/2022.2/lib/python3.8/", line 516, in run
    raise CalledProcessError(retcode, process.args,
    subprocess.CalledProcessError: Command '['run_dada_paired.R', '/scratch/lngor001/tmpxas0pfum/forward', '/scratch/lngor001/tmpxas0pfum/reverse', '/scratch/lngor001/tmpxas0pfum/output.tsv.biom', '/scratch/lngor001/tmpxas0pfum/track.tsv', '/scratch/lngor001/tmpxas0pfum/filt_f', '/scratch/lngor001/tmpxas0pfum/filt_r', '237', '179', '0', '14', '2.0', '2.0', '2', '12', 'independent', 'consensus', '1.0', '2', '1000000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/linux/rocky/8.x/x86_64/pkgs/qiime2/2022.2/lib/python3.8/site-packages/q2cli/", line 339, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/opt/linux/rocky/8.x/x86_64/pkgs/qiime2/2022.2/lib/python3.8/site-packages/qiime2/sdk/", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/opt/linux/rocky/8.x/x86_64/pkgs/qiime2/2022.2/lib/python3.8/site-packages/qiime2/sdk/", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/opt/linux/rocky/8.x/x86_64/pkgs/qiime2/2022.2/lib/python3.8/site-packages/q2_dada2/", line 292, 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.

Plugin error from dada2:

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

See above for debug info.

I also tried this to make sure
qiime tools validate demux_clean.qza
Result demux_clean.qza appears to be valid at level=max.

Hello @lyna,

From reading other posts with this error message, it seems like it's likely a problem with your computer's resources. Are you running this on a cluster or on your own machine?


1 Like

Hi @colinvwood ,
I'm running this on a cluster.


Do you know how much memory you're allocating to the job?

1 Like

I just found out that my organization is doing maintenance with the cluster. It should work after the maintenance is complete. Totally my fault for not remembering! Ay......Thanks for helping!!


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