Hello everyone, I’ve been having some trouble filtering my sequences using the dada2 command. The first time running, I got back an error message that read:
"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-mth5g2nm.log"
We used the following command:
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 149 --p-trunc-len-r 149 --p-n-threads 0 --p-max-ee 2.0 --p-trunc-q 2 --p-chimera-method ‘consensus’ --o-table table.qza --o-denoising-stats stats.qza --o-representative-sequences rep-seqs.qza
When running with the --verbose tag, we got back the following message:
"Command: run_dada_paired.R /tmp/tmpiyukm72i/forward /tmp/tmpiyukm72i/reverse /tmp/tmpiyukm72i/output.tsv.biom /tmp/tmpiyukm72i/track.tsv /tmp/tmpiyukm72i/filt_f /tmp/tmpiyukm72i/filt_r 149 149 0 0 2.0 2 consensus 1.0 0 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.1 / RcppParallel: 4.4.2
- Filtering …
- Learning Error Rates
150386892 total bases in 1009308 reads from 50 samples will be used for learning the error rates.
150386892 total bases in 1009308 reads from 50 samples will be used for learning the error rates. - Denoise remaining samples …
- 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/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
run_commands([cmd])
File “/home/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpiyukm72i/forward’, ‘/tmp/tmpiyukm72i/reverse’, ‘/tmp/tmpiyukm72i/output.tsv.biom’, ‘/tmp/tmpiyukm72i/track.tsv’, ‘/tmp/tmpiyukm72i/filt_f’, ‘/tmp/tmpiyukm72i/filt_r’, ‘149’, ‘149’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘0’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call
results = action(**arguments)
File “</home/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-451>”, line 2, in denoise_paired
File “/home/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/home/sjhustad/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 246, in denoise_paired
" and stderr to learn more." % e.returncode)
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."
We are sure that our samples are demultiplexed and that the forward and reverse reads are not identical, as some others reported in similar threads. We have 279 samples with forward and reverse barcodes that were imported using the Casava format. I have been using qiime2-2019.4. If anyone has any insight I would greatly appreciate it!