diversity alpha-rarefaction taking too long

User Support
1

I just switched to qiime2-amplicon-2024.5 installed through conda.

I am running diversity alpha-rarefaction. See my code below.

qiime diversity alpha-rarefaction
--i-table "../Qiime2Processed/asv_filtered.qza"
--p-max-depth 50000
--p-steps 2500
--m-metadata-file '../Metadata/metadata3.txt'
--o-visualization "../Qiime2Processed/asv_filtered-rarecurves.qzv"

It's taking so long. I haven't experienced this with older versions (i.e., 2021 and 2022 [when versions weren't amplicon-specific]).

Thank you!

2

hi @jbbq
What OS are you running this on?

This is alot of steps for qiime diversity alpha-rarefaction our default is 10. Doc Reference. This is why it is taking a long time.

How long do you mean when you say that its taking so long?
Could you do a little more digging for me? :mag:

  1. Have you run this same data in the older versions you mentioned?
  2. Did you run the same number of steps (--p-steps 2500) on the older versions?
  3. How long was that taking? (you can find this in the provenance)

Thank you! All this information will help us narrow down what the issue is!

1 Like
5

Thanks for your prompt response.

What OS are you running this on?

I'm running it in Ubuntu 20.04 LTS.

This is alot of steps for qiime diversity alpha-rarefaction our default is 10. Doc Reference. This is why it is taking a long time.

I thought the higher the value, the less time it would take (bigger range will be considered between my minimum and maximum depths). I might be wrong. Will re-do.

How long do you mean when you say that its taking so long?

I've been running it for half a day, so I stopped. I just made rarefaction curves from a different package.

  1. Have you run this same data in the older versions you mentioned?
  2. Did you run the same number of steps (--p-steps 2500) on the older versions?
  3. How long was that taking? (you can find this in the provenance)
  1. Not the same data, but I did have much bigger dataset that included 4 alpha metrics (faith's, observed, shannon & pielou's).
  2. Yes, I also used 2500.
  3. I already canceled my run so I can't be certain.
6

Hi @jbbq

This actually the number of times you sample. So our default is 10 meaning we will sample 10 times between max and min depths. Currently you are sampling 2500 times which will take longer.

I mean how long did it take in older versions of QIIME 2 if you ran it at 2500 steps. Did those ever finish?

2 Likes
7

It just took an hour or so. 2 hours tops.