2022.01.20 [bug note] | qiime2: an error was encoded while running dada2 in R (return code 1)

Project scenario ：

Version introduction ： qiime2：2021.4 DADA2：1.18.0 R：4.0.3 Project scenario ： Use qiime2 In the process , perform dada2 Command to classify the characteristic sequence of sequencing data , An error has occurred .

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Problem description ：

I haven't been right about qiime2 Updated or modified , The following error messages appear suddenly

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

After opening the log, you can find the key record of error reporting ：

R version 4.0.3 (2020-10-10)
 Load the required program package ：Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.8 / RcppParallel: 5.1.5
1) Filtering Error in validObject(.Object) :
  invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class  Stop executing  Traceback (most recent call last): File "/home/yangxin/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 266, in denoise_paired run_commands([cmd]) File "/home/yangxin/miniconda3/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/yangxin/miniconda3/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/tmprogiwn9c/forward', '/tmp/tmprogiwn9c/reverse', '/tmp/tmprogiwn9c/output.tsv.biom', '/tmp/tmprogiwn9c/track.tsv', '/tmp/tmprogiwn9c/filt_f', '/tmp/tmprogiwn9c/filt_r', '0', '0', '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/yangxin/miniconda3/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/yangxin/miniconda3/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/yangxin/miniconda3/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/yangxin/miniconda3/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.

Core sentence

invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class

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Cause analysis ：

We found that dada2 There may be two problems with the execution error report , First, there is a problem with the data input of the double ended sequence （ Whether to remove primers ）; Two is R package Matrix Version change , Lead to qiime2 Call error , My problem belongs to the latter .

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Solution ：

uninstall R package Matrix Reinstall the specified version 1.3.2

remove.packages("Matrix") # uninstall R package Matrix
install.packages("devtools")# Use devtools To install R Packages make it easier to search for resources 
devtools::install_version("Matrix", version = "1.3.2", repos = "http://cran.us.r-project.org")# install 1.3.2 edition 
packageVersion("Matrix")# Check after successful installation Matrix edition 

After the problem is solved, it will run normally .

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