Couldn't tell the DADA2 is stuck or still running

Hello All,

I tried to get the stats-dada2.qza and table-dada2.qza files through DADA2, but it’s around two days and nothing changed. I typed the commands just follow the tutorial. It looks like it still running but it’s already two days passed. No error message was shown. My input size is about 5GB. I can’t tell it’s stuck or it’s still running.

Commands:

qiime dada2 denoise-single \

–i-demultiplexed-seqs demux-single-end-with-Ted.qza
–p-trim-left 0
–p-trunc-len 100
–o-representative-sequences rep-seqs-dada2.qza
–o-table table-dada2.qza
–o-denoising-stats stats-dada2.qza

Thank you all,

Ziyi

Hi @Ziyi_Wang,

The denoising step in dada2 can be very time-consuming and its overall run-time depends on various factors, some of which are described here and here.
If no error message is shown it is likely just slowly working away. And days of run times are not unheard of. I would just let it run till completion. You can also open another terminal and type ‘top’ to see if the task is in fact still processing.
For future work though some strategies to massively improve the speed of this step:
Increase the number of cores you dedicate to the task by using the --p-n-threads INTEGER parameter in dada2. This will essentially split the job into n tasks which should in theory reduce the time for denoising by n times. If you are using a virtualmachine you may want to adjust your settings first to dedicate more processors and RAM to your virtual machine.
Good luck!

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