BUG:Can not run qiime dada2 denoise-ccs without primers or adapters about q2-dada2 HOT 6 OPEN

I haven't looked at this in detail, but offhand this seems like a good one for you to work on @hagenjp - this should just be modifying the --p-front and --p-adapter fields to not be required on the QIIME 2 side. Assigning this to you in case you want a break from all of your migration work, but no immediate rush on this!

from q2-dada2.

I had the same problem, but what puzzled me was why someone could run the code without writing those two parameters.

from q2-dada2.

Hi,
I am the first time user of Qiime and found this conversation as I too have problem using "qiime dada2 denoise-ccs". Here is the script I used
qiime dada2 denoise-ccs --i-demultiplexed-seqs ${dir}/demultiplexed-trimmed-single.qza --p-trim-left 20 --p-trunc-len 1600 --p-n-threads 20 --o-representative-sequences ${dir}/rep-seqs-dada2.qza --o-table ${dir}/table-dada-test1.qza --o-denoising-stats ${dir}/stats-dada2-test1.qza --p-front AGRGTTYGATYMTGGCTCAG --p-adapter AAGTCGTAACAAGGTARCY --verbose

And the error

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/sw/auto/rocky8c/epyc4/software/QIIME2/2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in denoise_ccs
File "/sw/auto/rocky8c/epyc4/software/QIIME2/2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/sw/auto/rocky8c/epyc4/software/QIIME2/2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/sw/auto/rocky8c/epyc4/software/QIIME2/2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 419, in denoise_ccs
raise Exception("An error was encountered while running DADA2"
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.

Thanks in advance for your help
Lida

from q2-dada2.

Hi @lida56, I'm not sure that this is related to this specific GitHub issue. Would you mind posting this with a request for help on the QIIME 2 Forum? We can help you troubleshoot this there.

from q2-dada2.