Hi, I’m using qiime2-2019.4 in MacOS.
I run dada2 with this command:
qiime dada2 denoise-paired
–i-demultiplexed-seqs paired-end-demux.qza
–p-trunc-len-f 270
–p-trunc-len-r 220
–p-trim-left-f 17
–p-trim-left-r 21
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza
–p-n-threads 0
and I get this 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.
#This is log file:
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/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/forward /var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/reverse /var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/output.tsv.biom /var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/track.tsv /var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/filt_f /var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/filt_r 270 220 17 21 2.0 2 consensus 1.0 0 1000000
R version 3.5.1 (2018-07-02)
Loading necessary packages: Rcpp
Error: package or namespace load failed for ‘Rcpp’ in rbind(info, getNamespaceInfo(env, “S3methods”)):
The number of columns in each matrix must match (see argument 2)
Error: package ‘Rcpp’ can not be loaded
Execution stopped
Traceback (most recent call last):
File “/Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
run_commands([cmd])
File “/Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/forward’, ‘/var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/reverse’, ‘/var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/output.tsv.biom’, ‘/var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/track.tsv’, ‘/var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/filt_f’, ‘/var/folders/vr/y6w275dn6kxb1g7txmbfzw6m0000gn/T/tmpsq6exit3/filt_r’, ‘270’, ‘220’, ‘17’, ‘21’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘0’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call
results = action(**arguments)
File “</Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-451>”, line 2, in denoise_paired
File “/Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/Users/mac/anaconda2/envs/qiime2-2019.4/lib/python3.6/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.
It would be great if anyone could guide me.