qiime dada2 denoise-ccs, Plugin error from dada2:

[kks_k]

Hello,
In qiime dada2 denoise-ccs, when i run this command line, the analysis of almost sample was performed well. But, some sample carried out some problems.

Well performed sample, the script was followed by..

But the other sample was followed by...

I can't understand which is the point i have to correct.
The script was performed followed by..
qiime dada2 denoise-ccs --i-demultiplexed-seqs single-end-demux.qza --p-front AGAGTTTGATCMTGGCTCAG --p-adapter TACGGYTACCTTGTTAYGACTT --p-min-len 1000 --p-max-len 1600 --p-n-threads 24 --o-table table --o-representative-sequences rep-seqs --o-denoising-stats stats --verbose

I hope you can help me out.

Thanks

(denoise-ccs: Denoise and dereplicate single-end Pacbio CCS — QIIME 2 2022.2.0 documentation)

[Keegan-Evans]

@kks_k,

Could you run

qiime dada2 denoise-ccs\
--i-demultiplexed-seqs single-end-demux.qza\
--p-front AGAGTTTGATCMTGGCTCAG\
--p-adapter TACGGYTACCTTGTTAYGACTT\
--p-min-len 1000\
--p-max-len 1600\
--p-n-threads 24\
--o-table table\
--o-representative-sequences rep-seqs\
--o-denoising-stats stats\
--verbose > denoising_error.txt 2>&1

to capture the stdout and stderror in the file denoising_error.txt(or whatever you want to call it!) and post the file here so we can get a better idea of what is going on?

So essentially run your original command and send all of the output information to that file. You can try copying and pasting, but sometimes whitespace errors can cause trouble with pasting commands. The important thing is to add > denoising_error.txt 2>&1 to the end of your command so that the relevant error information is captured.

[kks_k]

Thank you for your reply.
But, error description is not different above results i think.

Especially, return code-6 and "please inspect stdout and stderr to learn more" comments are not well searched in web.

Here, upload the denoising_error.txt
denoising_error.txt (2.7 KB)

[Oddant1]

Hello @kks_k, can you tell us what version of QIIME 2 you're running as well as what environment you're running it on (native linux, vm, hpc, etc.)? Additionally, do you have any other versions of R installed (RStudio or anything)? Thank you.