Long-running DADA2 issue

[bioinfo (Jan)]

Hi everyone,
I have similar doubts about dada2 runtime in qiime2.

Have a look at the picture, the dada2 processes on each thread are in "S" - sleep mode. I expect the program writes something on my HDD, but noone file in my qiime2_TMP folder has been updated from 36 hours.
Is there any solution to be sure that the process is running and it will finish some day?
Thanks for any help.

[thermokarst]

DADA2 can take a bit of time, it really depends on things like sequencing depth, number of samples, trimming/truncation parameters, etc. I would let it go for a few more days if I were you. Keep us posted!

[KEDIR_HAMZA]

Hi Everyone,
Dada2 denoise step is also taking longer time (6-days) for me. My current computer has 4-cores and 16GB RAM specification. I was planning to buy a computer with more core or high speed processor and more RAM size. Would this might help in speeding up dada2 denoise step? In other word, is dada2 denoise step of qiime2 multi-thread or single thread software?

Thanks,
Kedir

[thermokarst]

Hi @KEDIR_HAMZA!

@KEDIR_HAMZA

I was planning to buy a computer with more core or high speed processor and more RAM size. Would this might help in speeding up dada2 denoise step?

Most likely, although we can't really say for sure. In general though, having more resources should help.

@KEDIR_HAMZA

In other word, is dada2 denoise step of qiime2 multi-thread or single thread software?

q2-dada2 is DADA2 (it isn't a separate implementation). DADA 2 does support multi-threaded operation. Check out the q2-dada2 docs to see how that is exposed in Q2:

  --p-n-threads INTEGER           The number of threads to use for
                                  multithreaded processing. If 0 is provided,
                                  all available cores will be used.  [default:
                                  1]

Hope that helps!

[KEDIR_HAMZA]

Hi @thermokarst
Great!
Thanks a lot!

[ben (benjamin w.)]

Just FYI, we run DADA2 on a server takes about 24-72 hours, running several runs in parallel. This is a run of 182 samples with about 5,000-30,000 sampling depth per sample. This server has 64 gigs of memory, 1TB SSD, and an 8-core intel processor. On a laptop computer, it’s likely to take 3-4x that with a spinning HD and 8-16 gigs of RAM.