missing DADA2 output

[ltom (Lauren)]

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 also tried specifying an output directory:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-paired-end.qza
–p-trunc-len-f 240
–p-trunc-len-r 240
–output-dir dada2_out
–p-n-threads 8 &

Both attempts generate only one file: table.qza. How do I generate the other (2) files?

Thank you,
Lauren

[thermokarst]

Hi @ltom! I suspect the command is not running to completion, sometimes backgrounding a job (adding the & can make it tricky to tell when it is done. My recommendation is to try again, without backgrounding, and report back. Also, what version of QIIME 2 are you using?

[ltom (Lauren)]

I tried running without backgrounding and I think my run stalled (the resulting output directory is empty). I am trying once more using the following command:

qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-paired-end.qza
–p-trunc-len-f 240
–p-trunc-len-r 240
–output-dir dada2_out_v6
–p-n-threads 8

FYI, I am using the following version of QIIME 2:
qiime info

System versions
Python version: 3.6.7
QIIME 2 release: 2019.1
QIIME 2 version: 2019.1.0
q2cli version: 2019.1.0

Installed plugins
alignment: 2019.1.0
composition: 2019.1.0
cutadapt: 2019.1.0
dada2: 2019.1.0
deblur: 2019.1.0
demux: 2019.1.0
diversity: 2019.1.0
emperor: 2019.1.0
feature-classifier: 2019.1.0
feature-table: 2019.1.0
fragment-insertion: 2019.1.0
gneiss: 2019.1.0
longitudinal: 2019.1.0
metadata: 2019.1.0
phylogeny: 2019.1.0
quality-control: 2019.1.0
quality-filter: 2019.1.0
sample-classifier: 2019.1.0
taxa: 2019.1.0
types: 2019.1.0
vsearch: 2019.1.0

Application config directory
/users/ltom/.config/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org