Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
I was trying to denoise data from "PRJNA698459"
I've tried the following command to denoise the data,
qiime dada2 denoise-paired \
> --i-demultiplexed-seqs fondue-output/paired_reads.qza \
> --p-trunc-len-f 101 \
> --p-trunc-len-r 101 \
> --p-trim-left-f 0 \
> --p-trim-left-r 0 \
> --p-trunc-q 2 \
> --o-table fondue-output/dada2_table.qza \
> --o-representative-sequences fondue-output/rep_seq.qza \
> --o-denoising-stats fondue-output/dada2_stats.qza
But I got this error message,
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -9). Please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-v76jckuh.log
Here is the error report from mentioned 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.R --input_directory /tmp/tmp9ro06l51/forward --input_directory_reverse /tmp/tmp9ro06l51/reverse --output_path /tmp/tmp9ro06l51/output.tsv.biom --output_track /tmp/tmp9ro06l51/track.tsv --filtered_directory /tmp/tmp9ro06l51/filt_f --filtered_directory_reverse /tmp/tmp9ro06l51/filt_r --truncation_length 101 --truncation_length_reverse 101 --trim_left 0 --trim_left_reverse 0 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000
R version 4.2.2 (2022-10-31)
Loading required package: Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6
2) Filtering ......................................................................................................
3) Learning Error Rates
Traceback (most recent call last):
File "/home/turtle/miniconda3/envs/fondue/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/home/turtle/miniconda3/envs/fondue/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/turtle/miniconda3/envs/fondue/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmp9ro06l51/forward', '--input_directory_reverse', '/tmp/tmp9ro06l51/reverse', '--output_path', '/tmp/tmp9ro06l51/output.tsv.biom', '--output_track', '/tmp/tmp9ro06l51/track.tsv', '--filtered_directory', '/tmp/tmp9ro06l51/filt_f', '--filtered_directory_reverse', '/tmp/tmp9ro06l51/filt_r', '--truncation_length', '101', '--truncation_length_reverse', '101', '--trim_left', '0', '--trim_left_reverse', '0', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '1', '--learn_min_reads', '1000000']' died with <Signals.SIGKILL: 9>.During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/turtle/miniconda3/envs/fondue/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/turtle/miniconda3/envs/fondue/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/turtle/miniconda3/envs/fondue/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/turtle/miniconda3/envs/fondue/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 339, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
What can I do to correct this?
