Hi,
I am in the process of learning how to use qiime2 and I got an error when denoising with DADA2:
qiime dada2 denoise-paired \
--i-demultiplexed-seqs demultiplexed-sequences.qza
--p-trunc-len-f 204
--p-trim-left-r 1
--p-trunc-len-r 205
--o-representative-sequences asv-sequences-0.qza
--o-table feature-table-0.qza
--o-denoising-stats dada2-stats.qza
--verbose
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 /var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/forward /var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/reverse /var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/output.tsv.biom /var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/track.tsv /var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/filt_f /var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/filt_r 204 205 0 1 2.0 2.0 2 12 independent consensus 1.0 1 1000000
R version 4.1.2 (2021-11-01)
Loading required package: Rcpp
Error: package or namespace load failed for 'Rcpp' in library.dynam(lib, package, package.lib):
** shared object 'Rcpp.so' not found**
Error: package 'Rcpp' could not be loaded
Execution halted
Traceback (most recent call last):
File "/Users/laljxxxx/miniconda3/envs/qiime2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 266, in denoise_paired
run_commands([cmd])
File "/Users/laljxxxx/miniconda3/envs/qiime2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/laljxxxx/miniconda3/envs/qiime2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/forward', '/var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/reverse', '/var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/output.tsv.biom', '/var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/track.tsv', '/var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/filt_f', '/var/folders/36/2cm5rcw91rq1yl80f49j3kdr0000gn/T/tmp42ih8_qd/filt_r', '204', '205', '0', '1', '2.0', '2.0', '2', '12', 'independent', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 1.During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/laljxxxx/miniconda3/envs/qiime2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/Users/laljxxxx/miniconda3/envs/qiime2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/Users/laljxxxx/miniconda3/envs/qiime2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/Users/laljxxxx/miniconda3/envs/qiime2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 279, 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.
I am working on a Mac with chip M1 (using rosetta terminal), the qimme version is 2021.11.0 and the conda version 4.11.0.
I tried this to solve the problem, but anything worked:
- I manually installed "Rcpp" package in R.
- I updated R.
- I updated conda, cleaned the cache, delete the qiime2 environment and create it again.
Could you help me to figure out what I can do to solve the problem, please?
forum!