Qiime dada2 denoise-single: R process defunct

I’ve searched for an R process going defunct but I have not found anything.

I ran this command:

qiime dada2 denoise-single
–i-demultiplexed-seqs /home/rat_study_single_demux.qza
–p-trim-left 21
–p-trunc-len 290
–output-dir /home/dada2
–o-representative-sequences rep_seqs_dada2.qza
–o-table rat_study_single_table_dada2.qza
–o-denoising-stats rat_study_single_stats_dada2.qza
–p-n-threads 12 &

and each time I see an R process going defunct:

14775 pts/26 00:00:00 bash
15368 pts/26 00:00:08 qiime
15373 pts/26 04:08:57 R
15403 pts/26 00:02:40 R
22411 pts/26 00:00:00 ps

I am processing approximately 4M reads, and I have let it run for approximately 2 days in CPU time. Looking at some documentation, it seems like this should only take 2-10 CPU hours, so I’m wondering if this other R process (15373) is waiting on the defunct R process.

Hey there @weirdlob!

It looks like you are backgrounding your job (via the ampersand at the end of the command) - is it possible that the process is being orphaned when logging out of the compute node? Maybe try again without backgrounding --- use a job queue if available, otherwise try screen or tmux.

Happy QIIMEing! :qiime2:

Is it possible that running it in parallel is causing this?

I allowed it to run on a single processor overnight, backgrounded (&), and it completed successfully. This is great (it is not necessarily an immediate issue now), but I would like to be able to throw more power at this if I have larger data sets that need it.


Hmm, I don't think so, but if you wanted to pursue that you should check out the DADA2 issue tracker

More likely, in my opinion, is that the backgrounding is to blame here, and something else was different between your 12-thread and 1-thread runs, besides the thread count (for example, your shell session did end vs didn't end).

FWIW, I generally work with >1 threads from my own analyses and have had no issues, although I am using a job scheduler. I think I have generally observed success with multiple threads from other users here on the forum too, so I suspect that might be a bit of a red herring...

:qiime2: :t_rex:

Would running this on a ‘screen’ (linux) bypass this issue?

Yep, I think so! I also suggest tmux above, which is a similar tool.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.