Missing dada2 Output with and without &

[Nicholas_Bokulich]

Hi @clare,
I am guessing this is the topic you are referring to:

missing DADA2 output

Hello, I am trying to run DADA2. My run completes, but only outputs (1) file: table.qza I was expecting (3) files as output: representative-sequences.qza table.qza denoising-stats.qza Here is the command I am running: qiime dada2 denoise-paired –i-demultiplexed-seqs demux-paired-end.qza –p-trunc-len-f 240 –p-trunc-len-r 240 –o-representative-sequences representative-sequences.qza –o-table table.qza –o-denoising-stats denoising-stats.qza –p-n-threads 8 –verbose & I have als…

It looks like that user might have resolved their problem by outputting to a directory, instead of to individual filepaths... but they never wrote back to confirm that they found the missing outputs.

Would you like to try this command and see what happens?

qiime dada2 denoise-paired \
  --i-demultiplexed-seqs seqs.qza \
  --p-trim-left-f 0 \
  --p-trim-left-r 0  \
  --p-trunc-len-f 299 \
  --p-trunc-len-r 256 \
  --output-dir dada2_out