Silva in Qiime2-2020.8

[Marisa_Tello_Martin (Marisa Tello Martín)]

Hi everybody,
I have been working with greengens data base without problems with qimme2-2020.8 version. But when i use silva data base the run is killed. I have just dowload the data bases from the qiime 2 website so the scikit-learn version is fine.

Any idea what i am doing wrong?
Thank you in advance for all your help!
Best regards,
Marisa

[Nicholas_Bokulich]

Hello @Marisa_Tello_Martin!

@Marisa_Tello_Martin

Any idea what i am doing wrong?

Nothing! Classifiers trained on SILVA have much higher memory demands than Greengenes, being a much larger database. See this post for troubleshooting advice:

Feature-classifiers error

This is a memory error; essentially you do not have enough memory to open the SILVA classifier on your computer. This is low for the SILVA classifier — it will often take up to 32GB+ if left to its own devices! There’s a couple of things you might be able to do. First, you can use the --p-reads-per-batch parameter (e.g., set to 1000 or 2000) to reduce the number of reads classified at a time. However, it looks like you do not have enough memory to load the SILVA classifier, not the reads, s…

Good luck!

[Marisa_Tello_Martin (Marisa Tello Martín)]

Thank you Nicholas,
I thought there was another problem but you are right… i just have 16GB RAM…
Using the --p-reads-per-batch parameter doesn’t work either.
Is there any other option to run this with just 16GB RAM?
Thanks!

[Nicholas_Bokulich]

@Marisa_Tello_Martin

Using the --p-reads-per-batch parameter doesn’t work either.

I could get the SILVA classifier to work on my old laptop (8 GB) by using --p-reads-per-batch 2000 so I wonder if you do not really have 16GB available

Are you using virtual box or some other virtual machine? If so, you need to allocate more memory to the virtual machine, it is usually quite low by default (e.g., 1GB RAM) and is often a root cause of this error.

[Marisa_Tello_Martin (Marisa Tello Martín)]

@Nicholas_Bokulich

–p-reads-per-batch 2000

Hi again,
I am not using a virtual box but a standard pc with Ubuntu.
Using --p-reads-per-batch 1000 it does not work, i will try with 2000.
How can I know the memory it has allocate for this?
Sorry for bothering you, i am lost with this IT techs…
Marisa

[Nicholas_Bokulich]

@Marisa_Tello_Martin

Using --p-reads-per-batch 1000 it does not work, i will try with 2000.

if 1k fails, 2k will only do worse.

do you have other programs running concurrently? Maybe you should check memory use on your computer to make sure nothing is running in the background that is eating up RAM.

I’m not sure what else to say! You may need to either settle with a smaller database like greengenes or find a more powerful computer to use the SILVA classifier.