Dear qiime2 team,
I am using qiime2 2024.5 version.
I am trying to denoise my data using dada2 command, but facing a lot of errors. I have already tried many troubleshoots but not successful. Please check the following commands, I put in and the subsequent error messages I have received. I am also attaching the .qzv file as well to look for the basis of the error. Kindly help. Thanks and regards, Deepak
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired-end-demux.qza
--p-trunc-len-f 150
--p-trunc-len-r 150
--p-trim-left-f 10
--p-trim-left-r 10
--p-max-ee-f 2
--p-max-ee-r 2
--p-min-overlap 12
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
--verbose
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/tmp9ryirhbv/forward --input_directory_reverse /tmp/tmp9ryirhbv/reverse --output_path /tmp/tmp9ryirhbv/output.tsv.biom --output_track /tmp/tmp9ryirhbv/track.tsv --filtered_directory /tmp/tmp9ryirhbv/filt_f --filtered_directory_reverse /tmp/tmp9ryirhbv/filt_r --truncation_length 150 --truncation_length_reverse 150 --trim_left 10 --trim_left_reverse 10 --max_expected_errors 2 --max_expected_errors_reverse 2 --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 4.3.3 (2024-02-29)
Loading required package: Rcpp
DADA2: 1.30.0 / Rcpp: 1.0.12 / RcppParallel: 5.1.6
2) Filtering .
3) Learning Error Rates
12231380 total bases in 87367 reads from 1 samples will be used for learning the error rates.
12231380 total bases in 87367 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 "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 350, in denoise_paired
run_commands([cmd])
File "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 37, in run_commands
subprocess.run(cmd, check=True)
File "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmp9ryirhbv/forward', '--input_directory_reverse', '/tmp/tmp9ryirhbv/reverse', '--output_path', '/tmp/tmp9ryirhbv/output.tsv.biom', '--output_track', '/tmp/tmp9ryirhbv/track.tsv', '--filtered_directory', '/tmp/tmp9ryirhbv/filt_f', '--filtered_directory_reverse', '/tmp/tmp9ryirhbv/filt_r', '--truncation_length', '150', '--truncation_length_reverse', '150', '--trim_left', '10', '--trim_left_reverse', '10', '--max_expected_errors', '2', '--max_expected_errors_reverse', '2', '--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 "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in callable_executor
output_views = self._callable(**view_args)
File "/home/drdeepakkukkar/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 363, 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.
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.
paired-end-demux-summary.qzv (312.1 KB)
