BUG:Can not run qiime dada2 denoise-ccs without primers or adapters

[cherman2]

Improvement Description
We need to be able to run qiime dada2 denoise-ccs even if the data does not have primers or adapters. some users are receiving their data from sequencers without adapters, primers, and the sequences and merged

Current Behavior
qiime dada2 denoise-ccs requires --p-front and --p-adapter are required fields. Looking at the code, I believe this is something we are enforcing on the qiime2 interface side and it does not seem to be a requirement of dada2.

Proposed Behavior
Users on the forum have said that they are receiving data without primers and adapters and therefore can not run denoise-ccs

Comments

1. users does note that many sequences are not being classified because the sequences are reverse compliment.

References

1. Forum X-Ref

[lizgehret]

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!

[yongmingwang12syp]

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

[lida56]

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

[gregcaporaso]

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.

[colinvwood]

closed by #168

[colinvwood]

Reopening because we need to also support situations where both the forward and reverse primers have been removed. See here for an example.