Plugin error from dada2: An error was encountered while running DADA2 in R

qiime dada2 denoise-paired
--i-demultiplexed-seqs paired-end.qza
--p-trunc-len-f 240
--p-trunc-len-r 240
--p-n-threads 8
--p-chimera-method consensus
--p-min-fold-parent-over-abundance 8
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
--o-denoising-stats stats-dada2.qza 
Plugin error from dada2: 
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.  Debug info has been saved to /tmp/qiime2-q2cli-err-6rzifmpd.log

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/tmph8rjuegp/forward /tmp/tmph8rjuegp/reverse /tmp/tmph8rjuegp/output.tsv.biom /tmp/tmph8rjuegp/track.tsv /tmp/tmph8rjuegp/filt_f /tmp/tmph8rjuegp/filt_r 240 240 0 0 2.0 2.0 2 12 independent consensus 8.0 8 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
651360 total bases in 2714 reads from 2 samples will be used for learning the error rates.
651360 total bases in 2714 reads from 2 samples will be used for learning the error rates.
3) Denoise samples ..
..
4) Remove chimeras (method = consensus)
Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : 
  Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
Execution halted
Traceback (most recent call last):
  File "/home/dell/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 266, in denoise_paired
    run_commands([cmd])
  File "/home/dell/anaconda3/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/dell/anaconda3/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/tmph8rjuegp/forward', '/tmp/tmph8rjuegp/reverse', '/tmp/tmph8rjuegp/output.tsv.biom', '/tmp/tmph8rjuegp/track.tsv', '/tmp/tmph8rjuegp/filt_f', '/tmp/tmph8rjuegp/filt_r', '240', '240', '0', '0', '2.0', '2.0', '2', '12', 'independent', 'consensus', '8.0', '8', '1000000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/dell/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-514>", line 2, in denoise_paired
  File "/home/dell/anaconda3/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/dell/anaconda3/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/dell/anaconda3/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 think I know what is the issue is! Even though your error is happening in the chimera removal step, the issue may be about the number of input reads for step 2.

When you run this same command on a larger data set, does the plugin complete OK?

EDIT: If you have a small data set, check out Deblur. It comes with a pre-build error model so no training is needed.

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