Hello! I am running qiime2 2024.5 on a PC with paired-end demultiplexed sequences. I keep getting code 1 errors when running the following code. I tried decreasing my threads (from 0 to 15 to 8 to 4) as suggested in a previous post, but I keep getting an error. I have posted the command and verbose error. Any help would be greatly appreciated!
(qiime2-amplicon-2024.5) userselu@BI0326D00090294:~/Desktop/Students/CLB$ qiime dada2 denoise-paired --i-demultiplexed-seqs s12-correct-demux-paired-end-trimmed.qza --p-trunc-len-f 145 --p-trunc-len-r 132 --o-representative-sequences s12-rep-seqs.qza --o-table s12-table.qza --o-denoising-stats s12-denoising-stats.qza --verbose --p-n-threads 4
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/tmpneh5c27_/forward --input_directory_reverse /tmp/tmpneh5c27_/reverse --output_path /tmp/tmpneh5c27_/output.tsv.biom --output_track /tmp/tmpneh5c27_/track.tsv --filtered_directory /tmp/tmpneh5c27_/filt_f --filtered_directory_reverse /tmp/tmpneh5c27_/filt_r --truncation_length 145 --truncation_length_reverse 132 --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 4 --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
53592580 total bases in 369604 reads from 1 samples will be used for learning the error rates.
48787728 total bases in 369604 reads from 1 samples will be used for learning the error rates.
Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.
6: stop("Error matrix is NULL.")
5: getErrors(err, enforce = TRUE)
4: dada(drps, err = NULL, errorEstimationFunction = errorEstimationFunction,
selfConsist = TRUE, multithread = multithread, verbose = verbose,
MAX_CONSIST = MAX_CONSIST, OMEGA_C = OMEGA_C, ...)
3: learnErrors(filtsR, nreads = nreads.learn, multithread = multithread)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(learnErrors(filtsR, nreads = nreads.learn, multithread = multithread))
Traceback (most recent call last):
File "/home/userselu/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/userselu/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/userselu/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/tmpneh5c27/forward', '--input_directory_reverse', '/tmp/tmpneh5c27/reverse', '--output_path', '/tmp/tmpneh5c27_/output.tsv.biom', '--output_track', '/tmp/tmpneh5c27_/track.tsv', '--filtered_directory', '/tmp/tmpneh5c27_/filt_f', '--filtered_directory_reverse', '/tmp/tmpneh5c27_/filt_r', '--truncation_length', '145', '--truncation_length_reverse', '132', '--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', '4', '--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/userselu/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/userselu/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/userselu/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/userselu/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/userselu/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.
[https://view.qiime2.org/visualization/?src=9a65e45c-89c3-4839-9f94-1cc4d4ae10f3]
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