Hi I am having trouble running dada2, here is the code I input as part of the moving pictures tutorial:
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 --verbose
And here is part of the error message:
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in rbind(info, getNamespaceInfo(env, "S3methods")):
number of columns of matrices must match (see arg 2)
Execution halted
Traceback (most recent call last):
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 177, in _denoise_single
run_commands([cmd])
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/qiime2-archive-tnenva9b/ee0ddd31-47d3-435f-a143-68d7dc23daef/data', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/tmpl42q_mv0/output.tsv.biom', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/tmpl42q_mv0/track.tsv', '/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/tmpl42q_mv0', '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 "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-453>", line 2, in denoise_single
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 212, in denoise_single
band_size='16')
File "/Users/curanga/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 188, 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.
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.