error codes 9 and then 1 when running DADA2

[npj06]

I have also encountered a similar issue. I run dada2 with this command:qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trim-left-f 20 --p-trim-left-r 20 --p-trunc-len-f 0 --p-trunc-len-r 0 --o-representative-sequences rep-seqs.qza --o-table table.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
I got this error: **An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.**Command: run_dada.R --input_directory /var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/forward --input_directory_reverse /var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/reverse --output_path /var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/output.tsv.biom --output_track /var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/track.tsv --filtered_directory /var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/filt_f --filtered_directory_reverse /var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/filt_r --truncation_length 0 --truncation_length_reverse 0 --trim_left 20 --trim_left_reverse 20 --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 8 --learn_min_reads 1000000

R version 4.2.3 (2023-03-15)
载入需要的程辑包：Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6
2) Filtering Error in filterAndTrim(unfilts, filts, unfiltsR, filtsR, truncLen = c(truncLen, :
These are the errors (up to 5) encountered in individual cores...
Error in writeFastq(fqR, fout[[2]], "a", compress = compress) :
failed to write record 54785
Error in writeFastq(fqR, fout[[2]], "a", compress = compress) :
failed to write record 58660
Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
failed to write record 1032
Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
failed to write record 516
Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
failed to write record 11262
4: stop("These are the errors (up to 5) encountered in individual cores...\n",
rval)
3: filterAndTrim(unfilts, filts, unfiltsR, filtsR, truncLen = c(truncLen,
truncLenR), trimLeft = c(trimLeft, trimLeftR), maxEE = c(maxEE,
maxEER), truncQ = truncQ, rm.phix = TRUE, multithread = multithread)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(filterAndTrim(unfilts, filts, unfiltsR, filtsR,
truncLen = c(truncLen, truncLenR), trimLeft = c(trimLeft,
trimLeftR), maxEE = c(maxEE, maxEER), truncQ = truncQ,
rm.phix = TRUE, multithread = multithread))
Traceback (most recent call last):
File "/Users/nnnpj/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/Users/nnnpj/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/nnnpj/miniconda3/envs/qiime2-2023.5/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/forward', '--input_directory_reverse', '/var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/reverse', '--output_path', '/var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/output.tsv.biom', '--output_track', '/var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/track.tsv', '--filtered_directory', '/var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/filt_f', '--filtered_directory_reverse', '/var/folders//2kdh5xn16r94j2s72k05mlqr0000gn/T/tmpmictbzdz/filt_r', '--truncation_length', '0', '--truncation_length_reverse', '0', '--trim_left', '20', '--trim_left_reverse', '20', '--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', '8', '--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 "/Users/nnnpj/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 468, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/Users/nnnpj/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable
outputs = self.callable_executor(
File "/Users/nnnpj/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in callable_executor
output_views = self._callable(**view_args)
File "/Users/nnnpj/miniconda3/envs/qiime2-2023.5/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.

Thanks for your reply sincerely！

[npj06]

Previously, when I ran this DADA command, I received error 9. After running it again, I received error 1. The details were mentioned in my previous response. Thank you very much for your assistance. If you need any data from me, please let me know. Thank you.

[colinvwood (Colin Wood)]

Hello @npj06,

This error can happen when you run out of hard drive space. Check to see if that's the issue.

[npj06]

Thank you for your response. I will clean up my disk and try again.