I have a rather technical question, if qiime2 takes more than a day to execute a qiime dada2 donise-paired command, is it normal? or is something wrong?
Hi, Karina!
That question needs more data, i.e. what samples are you running, how many samples, how deep is the sequencing, and how many cores do you use for the process?
The answer will vary.
Cheers
Valentyn
4 Likes
Hi! thank you, are 24 samples each with its R1 and R2 , and the code: qiime dada2 denoise-paired --i-demultiplexed-seqs mrdna-puy.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 250 --p-trunc-len-r 250 --o-table table-mrdna.qza --o-representative-sequences rep-seqs-mrdna.qza --o-denoising-stats denoising-stats-mrdna.qza
and, how can I see how many cores I am working with?
The number of cores/threads is a parameter, look up --p-n-threads here: denoise-paired: Denoise and dereplicate paired-end sequences — QIIME 2 2022.8.3 documentation. It defaults to 1.
For 24 samples try to increase the number of cores by a reasonable amount and rerun it. It's hard to say how much it will take, but processing of 24 samples should not take more than 2-3 hours on most computers.
Also, you can check progress in a log file located within /tmp
Cheers
Valentyn
2 Likes
Thank you!!!!!!!!!!!!!1
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