Hello,
I’m trying to do an analysis of 454 data with DADA2 and I’m getting an error.
The code I’m running is:
qiime dada2 denoise-pyro
–i-demultiplexed-seqs demux-end.qza
–p-trunc-len 220
–p-n-threads 29
–o-table table
–o-representative-sequences rep-seqs
–verbose\
And this is the output I’m getting:
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering …
- Learning Error Rates
Initializing error rates to maximum possible estimate.
Error rates could not be estimated.
Error in err[c(1, 6, 11, 16), ] <- 1 :
incorrect number of subscripts on matrix
Calls: dada
Execution halted
Traceback (most recent call last):
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 152, in _denoise_single
run_commands([cmd])
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-4vum4tmw/f470feaf-64cc-4c05-a130-6f0ccc7687ce/data’, ‘/tmp/tmpy1z1xmt7/output.tsv.biom’, ‘/tmp/tmpy1z1xmt7/track.tsv’, ‘/tmp/tmpy1z1xmt7’, ‘220’, ‘0’, ‘2.0’, ‘2’, ‘Inf’, ‘consensus’, ‘1.0’, ‘29’, ‘250000’, ‘-1’, ‘32’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_pyro
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 367, in callable_executor
output_views = self._callable(**view_args)
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 268, in denoise_pyro
band_size=‘32’)
File “/home/fgplab/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 163, 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.
Can someone help me with this?