Greetings,
I’m new at qiime and I’m running the denoise step with dada2 out of a 2,5gb demur.qza file. It refers to 45 samples, full length 16S, pacbio sequel II platform.
The computer I’m using is quite good (64 cores, 512gb RAM) but it is taking very long (ow it is 90h and counting).
I’m monitoring the CPU activity with htop command and apparently it is running normally.
Since I have no previous experience, I’d like to know if anyone had done it with similar data and how long it took to compete.
Thank you in advance.
Hello @itainarataili,
Welcome to the forums! 
Would you be willing to send us a screenshot of your htop?
Also, can you post the command you ran, this will help us suggest possible improvements!
Hey @colinbrislawn thank you for your reply!
The command I used was:
qiime dada2 denoise-ccs
--i-demultiplexed-seqs demux.qza
--p-front AGAGTTTGATCMTGGCTCAG
--p-min-len 1400
--p-max-len 1600
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza \
And this is the htop command screenshot:
Here are the new docs for qiime dada2 denoise-ccs:
It looks like there's a n_threads setting which will let this run in parallel.
The top shows that only one thread is being used, or 99.8% of one thread.
Once you add --n-threads 32 the percent should be over 100% for parts of the pipeline.
The top shows a bunch of other Qiime processes that are 'sleeping'.
I'm not sure what's causing that!
Thank you very much for your response, I will try adjusting the –-n-threads.
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