Hello everyone, I’m getting the following error when I try to run the DADA2 denoising step (qiime 2018.4) with a small 16S dataset (2x150) on centos 7.
"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.“
We used the following command:
qiime dada2 denoise-paired \
--i-demultiplexed-seqs ./../PTH.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 0
--p-trunc-len-r 0
--p-n-threads 0
--o-table ./../result1/table.qza
--o-representative-sequences ./../result1/rep-seqs.qza
--o-denoising-stats ./../result1/stats.qza
When running with the --verbose tag, we got back the following message:
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_paired.R /tmp/tmph_4co0q7/forward /tmp/tmph_4co0q7/reverse /tmp/tmph_4co0q7/output.tsv.biom /tmp/tmph_4co0q7/track.tsv /tmp/tmph_4co0q7/filt_f /tmp/tmph_4co0q7/filt_r 0 0 0 0 2.0 2.0 2 independent consensus 1.0 0 1000000
R version 4.0.2 (2020-06-22)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.5 / RcppParallel: 5.0.2
- Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
These are the errors (up to 5) encountered in individual cores...
Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
failed to write record 467
Error in writeFastq(fqR, fout[[2]], "a", compress = compress) :
failed to write record 65940
Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
failed to write record 446
Execution halted
Traceback (most recent call last):
File "/home/wyf/.conda/envs/qiime2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 264, in denoise_paired
run_commands([cmd])
File "/home/wyf/.conda/envs/qiime2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/wyf/.conda/envs/qiime2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmph_4co0q7/forward', '/tmp/tmph_4co0q7/reverse', '/tmp/tmph_4co0q7/output.tsv.biom', '/tmp/tmph_4co0q7/track.tsv', '/tmp/tmph_4co0q7/filt_f', '/tmp/tmph_4co0q7/filt_r', '0', '0', '0', '0', '2.0', '2.0', '2', 'independent', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wyf/.conda/envs/qiime2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/wyf/.conda/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/wyf/.conda/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/wyf/.conda/envs/qiime2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 279, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I am running a small sample set with 3 samples .Anyone else have this problem ?
thanks in advance