train classifier

Hello. In the part of “train the classifier” it throws me this error --Plugin error fron feature-classifler: Unable to allocate array with shape (268435456,) and data type float64–. What can be ? Help me please
I use this command:

qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads ref-seqs.qza
–i-reference-taxonomy silva-138-99-tax.qza
–o-classifier classifier.qza

I suppose that you are running out of memory.
As suggested here, you can try to provide additional parameter --p-classify--chunk-size 20000 or lower to your command to reduce amount of memory required

Hi @Sandy_Arguello !
Here is another tutorial you can check to prepare reference sequences and train a classifier. It is very detailed and clear.

Thanks, I will do it

I installed qiime2 on another computer with 12 gigs of ram, and now it gives me this error "Plugin error from feature-classifier:
Unable to allocate 6.77 GiB for an array with shape (20000, 45450) and data type int64 "
It looks similar to the previous one!
I entered the suggested command and there was no change

It is highly possible that 12 gigs is not enough to train a classifier. Could you try to run it on a stronger machine or ask someone to do it for you? I think 32 Gb or 64 will work for you.

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Thanks, I’ll use another command for taxonomy.

Hi @Sandy_Arguello,
It looks like you are trying to train a classifier on the SILVA 138 database. This indeed can be a memory-intensive step — which is why we have already done it for you! You can download the pre-trained classifier and read more here: Data resources — QIIME 2 2021.4.0 documentation

(the tutorial that @timanix pointed you to explains the steps of how that classifier was created)

using the classifier to classify sequences is also memory-intensive, but a little bit less so… you can adjust the reads per batch to reduce memory load while running the classifier (search this forum for some more detailed troubleshooting advice)

Good luck!