dada2 error messages

[Paula_Azevedo]

Hi there, I used the following cmds and got the 6 errors below. Can you please help me to get it to work.

Thank you in advance, Paula.

qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza \ 
--p-trim-left-f 25 \
--p-trim-left-r 25 \
--p-trunc-len-f 240 \
--p-trunc-len-r 240 \
--o-representative-sequences rep-seqs.qza \
--o-table table.qza \
--o-denoising-stats denoising-stats.qza

 (1/6) Missing option '--p-trunc-len-f'.
 (2/6) Missing option '--p-trunc-len-r'.
 (3/6) Missing option '--o-table'.  ("--output-dir" may also be used)
 (4/6) Missing option '--o-representative-sequences'.  ("--output-dir" may
  also be used)
 (5/6) Missing option '--o-denoising-stats'.  ("--output-dir" may also be
  used)
 (6/6) Got unexpected extra argument ( )
zsh: command not found: --p-trim-left-f
zsh: command not found: --o-representative-sequences

Thank you so much, Paula.

[lizgehret]

Hi @Paula_Azevedo,

Welcome back to the forum!

It looks like there is an unescaped whitespace after the following parameter in your command:

--i-demultiplexed-seqs paired-end-demux.qza \

If you copy/paste the following command below (I've removed that whitespace for you), you should be all set!

qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza \
--p-trim-left-f 25 \
--p-trim-left-r 25 \
--p-trunc-len-f 240 \
--p-trunc-len-r 240 \
--o-representative-sequences rep-seqs.qza \
--o-table table.qza \
--o-denoising-stats denoising-stats.qza

Cheers

[Paula_Azevedo]

Thank you very much
Paula