Dada2 error

Hi
I ran Dada2 on a pair of forward and reverse reads of one sample. gives the following error:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

debug file contains:
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/tmpdyanzqav/forward --input_directory_reverse /tmp/tmpdyanzqav/reverse --output_path /tmp/tmpdyanzqav/output.tsv.biom --output_track /tmp/tmpdyanzqav/track.tsv --filtered_directory /tmp/tmpdyanzqav/filt_f --filtered_directory_reverse /tmp/tmpdyanzqav/filt_r --truncation_length 200 --truncation_length_reverse 200 --trim_left 5 --trim_left_reverse 5 --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
795990 total bases in 4082 reads from 1 samples will be used for learning the error rates.
795990 total bases in 4082 reads from 1 samples will be used for learning the error rates.
3) Denoise samples .
.
5) Remove chimeras (method = consensus)
Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) :
Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
3: stop("Input must be a valid sequence table.")
2: isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose)
1: removeBimeraDenovo(seqtab, method = chimeraMethod, minFoldParentOverAbundance = minParentFold,
allowOneOff = allowOneOff, multithread = multithread)
Traceback (most recent call last):
File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpdyanzqav/forward', '--input_directory_reverse', '/tmp/tmpdyanzqav/reverse', '--output_path', '/tmp/tmpdyanzqav/output.tsv.biom', '--output_track', '/tmp/tmpdyanzqav/track.tsv', '--filtered_directory', '/tmp/tmpdyanzqav/filt_f', '--filtered_directory_reverse', '/tmp/tmpdyanzqav/filt_r', '--truncation_length', '200', '--truncation_length_reverse', '200', '--trim_left', '5', '--trim_left_reverse', '5', '--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']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/root/anaconda3/envs/qiime2-2023.2/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 1), please inspect stdout and stderr to learn more.

I used many different trunc parameters for both forward and reverse reads but all of them failed with the same error.
Since i have just one sample (a pair of f and r seq files), So i can send my files to be checked at your end.

Hi
I ran Dada2 on a pair of forward and reverse reads of one sample on qiime2-2023.2 and it gave the following error:

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

debug file contains:
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/tmpdyanzqav/forward --input_directory_reverse /tmp/tmpdyanzqav/reverse --output_path /tmp/tmpdyanzqav/output.tsv.biom --output_track /tmp/tmpdyanzqav/track.tsv --filtered_directory /tmp/tmpdyanzqav/filt_f --filtered_directory_reverse /tmp/tmpdyanzqav/filt_r --truncation_length 200 --truncation_length_reverse 200 --trim_left 5 --trim_left_reverse 5 --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
795990 total bases in 4082 reads from 1 samples will be used for learning the error rates.
795990 total bases in 4082 reads from 1 samples will be used for learning the error rates.
3) Denoise samples .
.
5) Remove chimeras (method = consensus)
Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : 
  Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
3: stop("Input must be a valid sequence table.")
2: isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose)
1: removeBimeraDenovo(seqtab, method = chimeraMethod, minFoldParentOverAbundance = minParentFold, 
       allowOneOff = allowOneOff, multithread = multithread)
Traceback (most recent call last):
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
    run_commands([cmd])
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
    subprocess.run(cmd, check=True)
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpdyanzqav/forward', '--input_directory_reverse', '/tmp/tmpdyanzqav/reverse', '--output_path', '/tmp/tmpdyanzqav/output.tsv.biom', '--output_track', '/tmp/tmpdyanzqav/track.tsv', '--filtered_directory', '/tmp/tmpdyanzqav/filt_f', '--filtered_directory_reverse', '/tmp/tmpdyanzqav/filt_r', '--truncation_length', '200', '--truncation_length_reverse', '200', '--trim_left', '5', '--trim_left_reverse', '5', '--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']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in __call__
    results = action(**arguments)
  File "<decorator-gen-56>", line 2, in denoise_paired
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/root/anaconda3/envs/qiime2-2023.2/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 1), please inspect stdout and stderr to learn more.
I used many different trunc parameters for both forward and reverse reads but all of them failed with the same error.
Since i have just one sample (a pair of f and r seq files), So i can send my files to be checked at your end.

demux.qza (1.2 MB)

Hi
I ran Dada2 on a pair of forward and reverse reads of one sample on qiime2-2023.2 and it
demux.qza (1.2 MB)
gives the following error:

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

debug file contains:
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/tmpdyanzqav/forward --input_directory_reverse /tmp/tmpdyanzqav/reverse --output_path /tmp/tmpdyanzqav/output.tsv.biom --output_track /tmp/tmpdyanzqav/track.tsv --filtered_directory /tmp/tmpdyanzqav/filt_f --filtered_directory_reverse /tmp/tmpdyanzqav/filt_r --truncation_length 200 --truncation_length_reverse 200 --trim_left 5 --trim_left_reverse 5 --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
795990 total bases in 4082 reads from 1 samples will be used for learning the error rates.
795990 total bases in 4082 reads from 1 samples will be used for learning the error rates.
3) Denoise samples .
.
5) Remove chimeras (method = consensus)
Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : 
  Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
3: stop("Input must be a valid sequence table.")
2: isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose)
1: removeBimeraDenovo(seqtab, method = chimeraMethod, minFoldParentOverAbundance = minParentFold, 
       allowOneOff = allowOneOff, multithread = multithread)
Traceback (most recent call last):
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
    run_commands([cmd])
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
    subprocess.run(cmd, check=True)
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpdyanzqav/forward', '--input_directory_reverse', '/tmp/tmpdyanzqav/reverse', '--output_path', '/tmp/tmpdyanzqav/output.tsv.biom', '--output_track', '/tmp/tmpdyanzqav/track.tsv', '--filtered_directory', '/tmp/tmpdyanzqav/filt_f', '--filtered_directory_reverse', '/tmp/tmpdyanzqav/filt_r', '--truncation_length', '200', '--truncation_length_reverse', '200', '--trim_left', '5', '--trim_left_reverse', '5', '--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']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in __call__
    results = action(**arguments)
  File "<decorator-gen-56>", line 2, in denoise_paired
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/root/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/root/anaconda3/envs/qiime2-2023.2/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 1), please inspect stdout and stderr to learn more.
I used many different trunc parameters for both forward and reverse reads but all of them failed with the same error.
Since i have just one sample (a pair of f and r seq files), So i can send my files to be checked at your end.

Good morning @sajjad.sarikhan ,
This is the key line in your error message:

This error has been addressed many times on the forum — could you please search the forum archive (see the :mag: icon)? A large number of relevant posts have been written to help you troubleshoot this error.

Good luck!

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