DADA2 specifying output directory

Hi everyone - I’m about to run DADA2 as follows:

cd $WORK/Data/MSQ92/2_fastq

qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–p-trim-left-f 13
–p-trim-left-r 13
–p-trunc-len-f 140
–p-trunc-len-r 140
–p-n-threads 32
–o-representative-sequences rep-seqs-dada.qza
–o-table table-dada.qza
–o-denoising-stats stats.qza \

I would like to specify the directory so that the rep-seqs-dada.qza and table-dada.qza files go to another folder called Merged_runs in my main Data folder.

I’ve tried using --output-dir Merged_Runs but it doesn’t work.

I’m stuck - any help would be much appreciated. Thanks!

Try --output-dir $WORK/Data/Merged_Runs/

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