Denoising code qiime2-2022.2

I am working on code pasted below:
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --o-table table.qza --o-representative-sequences reps-seqs.qza --p-trunc-len-f 270 --p-trunc-len-r 220 --o-denoising-stats denoising-stats.qza

I am not getting any error message with this but, its taking forever to run on terminal (Mac). Is there something wrong with my code? I have a total of 40 sequences, is it expected to run past 6 hours?


Hi @rr220,

If you are not seeing an error then it is probably just still working, though 6 hrs is rather high for most datasets. What QIIME 2 version are you using? How much memory does your environment have access to? You can also run DADA2 in parallel using the --p-n-threads option to increase the number of threads you want to dedicate to the task.

40 sequences is rather impossibly low, can you explain what exactly you are referring to here? Do you mean 40 samples? Where did you get this number from?


Sorry I didn't phrase my question correctly. I have total 40 samples - so 80 FASTQ files. The run is just got done and it took 8 hours. I am using qiime2-2022.2 version. Memory capacity of my mac is 32 GB 2667 MHz.

Can you explain what you mean by "using the --p-n-threads option to increase the number of threads you want to dedicate to the task" ? I am new to this and still trying to figure things out

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Hi @rr220,

The --p-n-threads parameter allows you to tell DADA to use multiple threads from your CPU. So instead of all the process being done by one unit of "processor" it will be divided by n numbers that will run in parallel, effective reducing the time by n folds. You can see all the details on DADA2 parameters (in your case denoised paired) here:

And 40 samples sounds better, though that by itself is not predictive of how long your run will take, rather how many reads there are in total. But, I'm glad it completed never the less and now you know for future! Good luck, happy Qiimin'

Thanks a lot for your explanation. I appreciate your suggestions and help with this.

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