Hey all,
I am actually encountering a similar error as Byron. I was trying to go through the moving pictures tutorial as it is. When running the sequence quality control and feature table construction step using DADA2i.e;
(qiime2-2018.8) ltmfai001@srvslshpc617:/researchdata/fhgfs/ltmfai001/qiime2-moving-pictures-tutorial> *qiime dada2 denoise-single *
*> --i-demultiplexed-seqs demux.qza *
*> --p-trim-left 0 *
*> --p-trunc-len 120 *
*> --o-representative-sequences rep-seqs-dada2.qza *
*> --o-table table-dada2.qza *
> --o-denoising-stats stats-dada2.qza
I get the following error;
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-zqpn_aor.log
Looking at the log file, this is what it says;
(qiime2-2018.8) ltmfai001@srvslshpc617:/researchdata/fhgfs/ltmfai001/qiime2-moving-pictures-tutorial> more /tmp/qiime2-q2cli-err-zqpn_aor.log
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_single.R /tmp/qiime2-archive-i1rm_rfn/af321e99-b9e1-438e-9d84-2fe096d73fa9/data /tmp/tmphlsuclai/output.tsv.biom /tmp/t
mphlsuclai/track.tsv /tmp/tmphlsuclai 120 0 2.0 2 Inf consensus 1.0 1 1000000 NULL 16
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
Error: package ‘Rcpp’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Execution halted
Traceback (most recent call last):
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 152, in _denoise_single
run_commands([cmd])
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-i1rm_rfn/af321e99-b9e1-438e-9d84-2fe096d73fa9/data’, ’
/tmp/tmphlsuclai/output.tsv.biom’, ‘/tmp/tmphlsuclai/track.tsv’, ‘/tmp/tmphlsuclai’, ‘120’, ‘0’, ‘2.0’, ‘2’, ‘Inf’, ‘consensus’, ‘1.0’, ’
1’, ‘1000000’, ‘NULL’, ‘16’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_single
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 186, in denoise_single
band_size=‘16’)
File “/home/ltmfai001/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 163, in _denoise_single
" 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.
Now when I run this process using deblur, everything works out just fine.
I had the same problem while running with Qiime2-2018.6 version. I thought upgrading to the latest version could solve the problem, but nah!
I am encountered a similar problem when running my sequences. I believe once I solve the problem while running the tutorial everything should work out fine with my data as well, I hope!
Can someone please help!
Thank you