– Hi,
I use last version of qiime 2 (qiime2-2018.11), and running dada2 step it failed with:
R version 3.4.1 (2017-06-30)
The loading required the package: Rcpp
Error: package or namespace load failed for ?dada2?
Functions that are not generic S4 are found when exporting methods from the?IRanges? namespace. ?endoapply?, ?mendoapply?
Execution stopped
Traceback (most recent call last):
File “/home/toto/.conda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
run_commands([cmd])
File “/home/toto/.conda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/toto/.conda/envs/qiime2-2018.11/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmp1j83cbqb/forward’, ‘/tmp/tmp1j83cbqb/reverse’, ‘/tmp/tmp1j83cbqb/output.tsv.biom’, ‘/tmp/tmp1j
83cbqb/track.tsv’, ‘/tmp/tmp1j83cbqb/filt_f’, ‘/tmp/tmp1j83cbqb/filt_r’, ‘0’, ‘0’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘16’, ‘1000000’]’ returned non-zero exit
status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/toto/.conda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/home/toto/.conda/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/toto/.conda/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/home/toto/.conda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 246, 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.
How to pass this step ?
thank you –