I installed qiime2 2022.8 on macOS conda native installation. I have an M1 mac with 16 GB RAM.
when i run the Moving Pictures and Atacama tutorials, I get an error at the DADA2 step (but the Deblur option works in the Moving Pictures tutorial).
This is the error in the log file, which suggests that the R installation lacks Rcpp
cat /var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/
T/qiime2-q2cli-err-ghjj4s92.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 fil
es that no longer exist.
Command: run_dada.R --input_directory /var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/forward --inpu
t_directory_reverse /var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/reverse --output_path /var/folde
rs/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/output.tsv.biom --output_track /var/folders/s1/wpx8hzv51s9441b
4gxsrd_7w0000gn/T/tmpik5ces91/track.tsv --filtered_directory /var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmp
ik5ces91/filt_f --filtered_directory_reverse /var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/filt_r
--truncation_length 150 --truncation_length_reverse 150 --trim_left 13 --trim_left_reverse 13 --max_expected_erro
rs 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independe
nt --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 100
0000
R version 4.2.0 (2022-04-22)
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/douglasyu/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line
308, in denoise_paired
run_commands([cmd])
File "/Users/douglasyu/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line
36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/douglasyu/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/var/folders/s1/wpx8hzv51s9441b4gxsr
d_7w0000gn/T/tmpik5ces91/forward', '--input_directory_reverse', '/var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T
/tmpik5ces91/reverse', '--output_path', '/var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/output.tsv.
biom', '--output_track', '/var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/track.tsv', '--filtered_di
rectory', '/var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/filt_f', '--filtered_directory_reverse',
'/var/folders/s1/wpx8hzv51s9441b4gxsrd_7w0000gn/T/tmpik5ces91/filt_r', '--truncation_length', '150', '--truncatio
n_length_reverse', '150', '--trim_left', '13', '--trim_left_reverse', '13', '--max_expected_errors', '2.0', '--ma
x_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', '1', '--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/douglasyu/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 33
9, in __call__
results = action(**arguments)
File "<decorator-gen-291>", line 2, in denoise_paired
File "/Users/douglasyu/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line
234, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/Users/douglasyu/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line
381, in _callable_executor_
output_views = self._callable(**view_args)
File "/Users/douglasyu/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line
321, 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.