Missing dada2 Output with and without &

Hello, I have read through a previous post with a similar topic name but didn’t find how the issue was resolved. I have tried to run dada2 several times using the following:

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
–o-table table.qza
–o-representative-sequences rep_seqs.qza
–o-denoising-stats denoising_stats.qza

I have run it both with and without & on the end. Every time I have run it either way, I have only gotten the table.qza output. While it is running, I have been able to see that it is running using the top command but once the table appears in my directory, top no longer shows any qiime2 command running. It seems like the command is stopping after generating the table.qza. How can I get the full command to run?

My system versions are the following:
Python version: 3.6.7
QIIME 2 release: 2019.7
QIIME 2 version: 2019.7.0
q2cli version: 2019.7.0

Thank you for your time and attention to this!

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

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

Hi @Nicholas_Bokulich,

Ok, thank you. I will try that command and report back.

Hi again,

I have run that command and had the same result, only with the table.qza in a directory instead. Any idea why this might be happening? It seems to just stop after the table is generated.

Thank you,

Any chance you can provide the --verbose output?

I didn’t add --verbose but can run it again with that on the end if that would be helpful.

We need more information in order to help you — starting with --verbose will give us something to start with.

Ok - I’ll run that and get back to you when it finishes.

Thanks for your patience with my newness to this!

1 Like

Hello again,

I ran the same command with verbose and it ended up running just fine and created all three outputs. I haven’t figured out why this made any difference but if people have ideas, please let me know. I’d like to understand what happened and it may be helpful if someone has this issue again at some point.


Thanks for following up! The addition of the --verbose flag almost certainly had no bearing on the results. My best guess is that something “interrupted” the process the first time you ran it, and so the command was terminated before all the outputs were written. Just a theory at this point.