Plugin error from dada2 in jupyter notebook

[Gordon_Zheng]

Hi,

Each time I am running the first line of DADA2 command denoise-paired with the following citereia

  --p-trim-left-f 19 \
  --p-trim-left-r 20 \
  --p-trunc-len-f 186 \
  --p-trunc-len-r 186 \

And I keep getting the same error even when changing the trunc. Any suggestions?

Command: run_dada_paired.R /tmp/tmptqhtz21e/forward /tmp/tmptqhtz21e/reverse /tmp/tmptqhtz21e/output.tsv.biom /tmp/tmptqhtz21e/track.tsv /tmp/tmptqhtz21e/filt_f /tmp/tmptqhtz21e/filt_r 186 186 19 20 2.0 2.0 2 12 independent consensus 1.0 1 1000000

R version 4.1.3 (2022-03-10)
Loading required package: Rcpp
DADA2: 1.22.0 / Rcpp: 1.0.8.3 / RcppParallel: 5.1.5

1. Filtering ..............................
2. Learning Error Rates
   90844159 total bases in 543977 reads from 30 samples will be used for learning the error rates.
   90300182 total bases in 543977 reads from 30 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 "/nas/longleaf/rhel8/apps/qiime2/2022.2/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 279, in denoise_paired
   run_commands([cmd])
   File "/nas/longleaf/rhel8/apps/qiime2/2022.2/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
   subprocess.run(cmd, check=True)
   File "/nas/longleaf/rhel8/apps/qiime2/2022.2/miniconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
   raise CalledProcessError(retcode, process.args,
   subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmptqhtz21e/forward', '/tmp/tmptqhtz21e/reverse', '/tmp/tmptqhtz21e/output.tsv.biom', '/tmp/tmptqhtz21e/track.tsv', '/tmp/tmptqhtz21e/filt_f', '/tmp/tmptqhtz21e/filt_r', '186', '186', '19', '20', '2.0', '2.0', '2', '12', 'independent', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 1.

Traceback (most recent call last):
File "/nas/longleaf/rhel8/apps/qiime2/2022.2/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/nas/longleaf/rhel8/apps/qiime2/2022.2/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/nas/longleaf/rhel8/apps/qiime2/2022.2/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/nas/longleaf/rhel8/apps/qiime2/2022.2/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", 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.

[colinbrislawn (Colin J Brislawn)]

Hello Gordon,

Welcome to the forums!

Here's the core of your error:

Remove chimeras (method = consensus)
Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) :
Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
Execution halted

You can search the forums for that error.

It looks like that can happen when few or none of your reads are able to merge, then the following step of chimera removal fails.

Try upping the two --p-trunc-len* settings!