I also have another question. How long takes the dada2 denoise-paired to run for 2.8 million reads?
By the time I made this post, dada2 has been running for 8 hours.
I´m runing QIIME2 in a virtual Machine with 3Gb of RAM assignet to it.
Hi @Vixer,
I don’t have a good estimate on that, as many factors can influence runtime. It can often take a couple days to run dada2 on a very large dataset, but 2.8 million reads should probably take less time.
If it has not completed yet, you should check on the memory use to make sure you’re not running out, causing the job to lag (it would probably fail with a MemoryError first).
In my experience, Dada2 was running even 2-3 days (8GB Ram) in a virtual Machine (qiime2 v.11).
The same dataset was running for about 4-5 ours on the same PC in Dada2 using R instead of VM.
VM is generally much slower.
However the current (12) version of Q2 has propably better performance.
I would recommend using dada2 protocol on windows in RStudio, and then move results to qiime2 and finish experiment.
Here is a solution:
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