How many steps are there in the DADA2 process?

dada2

(Alyssa Fowlds) #1

I inputted the below command to perform a DADA2 filtering analysis and I have received the outputs up to “selfConsist step 5”.
How many steps are there in the process so I know how far along I am and and how much more I still need to wait for?

(qiime2-2018.11) dhcp-v018-082:~ alyssafowlds$ qiime dada2 denoise-single \

–i-demultiplexed-seqs single-end-demux.qza \

–p-max-ee 3 \

–p-n-reads-learn 800000 \

–o-table single-end-table.qza \

–o-representative-sequences single-rep-seqs.qza \

–p-trunc-len 0 \

–verbose


(Mehrbod Estaki) #2

Hi @Alyssa_Mariee,
The selfConsist steps don’t really refer to a finite # of steps that DADA2 goes through, those have to do with the error model training steps and denoising and it differs based on the # of number reads and # of samples as well as their distribution.
As far as how long DADA2 takes, unfortunately there is no real estimate since there are many factors at work here mainly the total number of reads you have and their length, your processing power and memory, the number of threads you assign to the task etc. It is probably the longest step in a typical analysis so be patient with it.
In the future you may wish to utilize the --p-n-threads option which should significantly (almost linearly) increase processing time.