Hi,
I'm running dada2 denoised-single on my simulated reads and received this error.
This is what I ran:
qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trunc-len 0 --output-dir qiimeoutput --verbose
Here is the error message:
Command: run_dada_single.R /tmp/qiime2-archive-45am8816/aa5c4cd2-2cd0-4fff-ba1e-eceaa3bcf57c/data /tmp/tmpavmzk2yk/output.tsv.biom /tmp/tmpavmzk2yk/track.tsv /tmp/tmpavmzk2yk 0 0 2.0 2 Inf independent consensus 1.0 1 1000000 NULL 16
R version 4.0.2 (2020-06-22)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.5 / RcppParallel: 5.0.2
- Filtering ..................................................
- Learning Error Rates
12554918 total bases in 63847 reads from 50 samples will be used for learning the error rates.
Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.
Execution halted
Traceback (most recent call last):
File "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 181, in _denoise_single
run_commands([cmd])
File "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/tmp/qiime2-archive-45am8816/aa5c4cd2-2cd0-4fff-ba1e-eceaa3bcf57c/data', '/tmp/tmpavmzk2yk/output.tsv.biom', '/tmp/tmpavmzk2yk/track.tsv', '/tmp/tmpavmzk2yk', '0', '0', '2.0', '2', 'Inf', 'independent', '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 "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_single
File "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 218, in denoise_single
band_size='16')
File "/data/wjw5274/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 192, 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.
I looked at posts with similar issues but could not find a suitable solution. Most of the posts I found have issues with merging forward and reverse, which is not the case here. Also tried adjusting --p-trunc-len and --p-trim-left, to no avail.
My question is, is "Error rates could not be estimated (this is usually because of very few reads)." the key issue here? Should I perhaps rerun my read simulation to have longer read length (if so, what's a suitable read length)? Or is it something I can fix by adjusting dada2 options?
Thank you so much! Appreciate your help.