Issue running code for Dada2/denoise

[arjunc (arjun chapagain)]

Hi
I am new to Qiime. I succeeded in importing the file, and now I want to trunc and trim (both forward and reverse reads from demultiplexed paired end data) about 250 from each read. I used the following parameters:
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired-end.qza
--p-trim-left-f 10
--p-trunc-len-f 280
--p-trim-left-r 10
--p-trunc-len-r 200
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza \

It is taking longer than expected. I haven't gotten output even after 2 days of running; however, I got results when I chose 120 f( 120 vs 280 or 200).
My amplicon size are 411 and my data were from Miseq 300 cycles ( demultiplexed paired end).

[timanix (Timur Yergaliyev)]

Welcome to the forum!

@arjunc

It is taking longer than expected. I haven't gotten output even after 2 days of running

Yes, it is long! But that time depends on a number of features and their frequencies, so it may take a long time to process. Check out if running dada2 in the multithread mode will decrease running time.

@arjunc

however, I got results when I chose 120 f( 120 vs 280 or 200).
My amplicon size are 411 and my data were from Miseq 300 cycles

What about the results you got? If you truncate your reads too short, they will fail to overlap and will not be merged, leading to a significant loss in the number of retained features. But it will run faster, that is correct.

If you lost a lot of reads, I can suggest you run it with truncating parameters 260 for F and 200 for R, but this time add more cores/threads (check out dada2 options).

Best,