Dear all,
I’m moving from qiime1 to qiime2. So, I try to run the analysis with the demo data “Moving Pictures” tutorial first. But unfortunately, I stuck in the denoise step. There are several similar question on the Forum. Only one is the same as mine. But the question was not solved.
Here is the command:
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
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-twf75dc2.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-qpt8h0jt/23109903-0ad5-408f-b6c5-e049dcbe41c8/data /tmp/tmpp9h4i9h7/output.tsv.biom /tmp/tmpp9h4i9h7/track.tsv /tmp/tmpp9h4i9h7 120 0 2.0 2 Inf consensus 1.0 1 1000000 NULL 16
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
Error: package or namespace load failed for ‘Rcpp’:
package ‘Rcpp’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Error: package ‘Rcpp’ could not be loaded
Execution halted
Traceback (most recent call last):
File “/home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 154, in _denoise_single
run_commands([cmd])
File “/home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-qpt8h0jt/23109903-0ad5-408f-b6c5-e049dcbe41c8/data’, ‘/tmp/tmpp9h4i9h7/output.tsv.biom’, ‘/tmp/tmpp9h4i9h7/track.tsv’, ‘/tmp/tmpp9h4i9h7’, ‘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/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-457>”, line 2, in denoise_single
File “/home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 189, in denoise_single
band_size=‘16’)
File “/home/jiaxu/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 165, 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.
I would appreciate it if anyone could help me with this.
Best regards,
Claire