Hello,
I’m currently working with 96 paired-end patient samples (192 files in total, totaling 66 GB). When I run DADA2, the process takes about a month to complete. My virtual machine is equipped with 32 threads and 128 GB of memory.
Wow!
What is your primer region out of curiosity?
Sequencing of 16S rRNA amplicons (using V3-V4 primers)
That's a really surprising amount of sequence data. I take it you are providing the --p-threads param and not doing anything with the pooling parameter? If you post your exact command, we may be able to better comment.
You may need to switch out of QIIME 2 and follow this approach:
https://benjjneb.github.io/dada2/bigdata.html
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