DADA2 running for over 4 days?

[Shruthi]

Hi everyone,

I am stuck at the dada2 stage where the commands are running for over 4 days now and still no output.This is the command I used:

qiime dada2 denoise-paired \

--i-demultiplexed-seqs analysis/demux-paired-end.qza
--p-trim-left-f 7
--p-trim-left-r 7
--p-trunc-len-f 298
--p-trunc-len-r 256
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza

My reads are 2 x 300 paired end reads (Miseq run: I got around 14.5 Million reads for 24 samples) and I am running qiime2-2019.1 in ubuntu in server (.ssh). Now, I know several people have had similar issues with the run time of dada2 but I was wondering whether it will ever give an output since its been over 4 days since I started the run.

Your comments are much appreciated.
Thanks.

[thermokarst]

Hi @Shruthi, 4 days is not unreasonable, especially considering you aren’t running with more than 1 thread (--p-n-threads n). See https://benjjneb.github.io/dada2/bigdata.html#how-long-does-it-take for more details.

[Shruthi]

Hi @thermokarst, thanks for the reply. Should I try opening another terminal and run alongside the old one increasing the number of threads? Will that be faster?

Thanks!

[timanix (Timur Yergaliyev)]

I think you can do it, but, in my opinion, it would be better to restart the whole process with indicating the number of threads or to wait until your current run will finish.

[Shruthi]

Yeah! I have restarted the run assigning 12 threads! It’s been running for over 12 hours now! Hopefully, this is faster than the last time.