qiime dada2 denoise-paired --help" for help.


I used my denosiing script on my 16S data and it failed. The error that I am getting is

denoise paired end for Afaf
Usage: qiime dada2 denoise-paired [OPTIONS]
Try "qiime dada2 denoise-paired --help" for help.

Error: no such option: --p-max-ee-f

Here is the code I used
qiime dada2 denoise-paired --i-demultiplexed-seqs 16S_demux.qza/per_sample_sequences.qza --p-n-threads 28 --p-max-ee-f 2.0 --p-max-ee-r 2.0 --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 0 --p-trunc-len-r 0 --o-representative-sequences 16S_rep-seqs-dada2_f1.qza --o-table 16S_table-dada2_f1.qza --o-denoising-stats 16S_stats-dada2_f1.qza --verbose

I already checked and the command --p-max-ee-f 0 is available in qiime2-2022.8 (which is the version I am using)

Please guide me through this, how can the command be available in the qiime2 version and yet I am getting an error that says it is not available

Hi @Afaf,

Thanks for reaching out!

I suspect there may be a stray whitespace character or something else of that nature going on here - can you run the following command and copy/paste the entire output in your response?

qiime dada2 denoise-paired --help

Additionally, can you copy/paste your entire command and the output in your response as well? Make sure that you are copying the entire code block from the beginning of your command to the end of the error message. Thanks! :lizard:

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