Log for a running DADA2?

[Oscar]

Hi all.

I am using QIIME2-2018.2 in Linux and running dada2 to 11 paired end samples using dada2 denoise-paired. First I run it with a small subsamples to see if everything was ok and it took around 20 min. Now I am running my real samples and it’s been 5 days so far. Is there a way to get a log of the running process? Command top shows R is running almost 100% and monitor system shows CPU1: 100%. But I would like to know in which step or how many samples have been processed so far, to decide if I should terminate it and try something else. Is that possible? When I use debur a log is created and the running process can be examined, but not sure if dada2 does.

Thank you,

Oscar

[Nicholas_Bokulich]

Hi @Oscar,
To have dada2 produce a log, append the --verbose flag to the end of your command. It looks like work is afoot to make it produce a log as a visualization, similar to deblur, so stay tuned for more details.

dada2 can take a long time to run — number of sequences, errors, length, etc are some of the numerous factors involved — so hang in there!

[Oscar]

Thanks for the help!