DADA2 in MacOS terminal and Windows Subsystem for Linux

When I running DADA2 in MacOS terminal and Windows Subsystem for Linux, I found that running dada2 on the MacOS terminal (600 min) is much slower than the Windows Subsystem for Linux (192 min) .

time qiime dada2 denoise-paired
–i-demultiplexed-seqs …/paired-end-demux.qza
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 200
–p-trunc-len-r 200
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza
–p-n-threads 0

214 samples and 515F-907R

My Windows 10: Intel® Core™ i5-9300H CPU @ 2.40GHz 2.40 GHz, RAM: 16GB
My MacOS: High Sierra, 3 GHz Intel Core i7, 16GB

Hello @kwb0207,
Welcome to the Forum :qiime2: !!
A helpful tip: there was not really a question in your post, Forum posts that do not have clear questions may spend longer waiting for a response :+1:.

I believe that dada2 taking longer on the mac isn't a QIIME2 issue. I believe it is based on the amount of threads that you can run on each computer. I looked up the CPU information that you provided. The windows has 12 available threads and the mac has 8.
If you look up the dada2 paired docs and you can see that if 0 is provided all availabe cores will be used.

--p-n-threads INTEGER The number of threads to use for multithread processing. If 0 is provided, all available cores will be used.

So since your computers have different available threads and you provided 0, dada2 is using all available cores and running faster on the one that can handle more threads.
I hope that clears things up!
Chloe :turtle:


OK,thank you very much!!

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