Hi! When I used q2-feature-classifier to train a classifier, I found an error: Unable to allocate array with shape (20000, 5391) and data type int64. Does anyone know the causation and how to solve this problem? Thanks very much!

Hello @Zhanzhan , Welcome to the Qiime 2 forums! :qiime2: The "Unable to allocate array" error means you don't have enough memory / RAM on your computer or in your virtual box to train the classifier. Training a taxonomic classifier takes a lot of RAM! How much RAM / memory do you have now? How la…

Hello, @colinbrislawn ! Thank you for your reply! I used greegene database: 99_otus.fasta and 99_otu_taxonomy.txt to train a classifier. Here is my code to produce a V4 ref-seqs.qza: qiime feature-classifier extract-reads \ --i-sequences 99_otus.qza --p-f-primer GTGTGYCAGCMGCCGCGGTAA --p-r-pr…

Hello again, I've edited your post a little bit. When you do a quote with > you need one extra line after to show the next text starts a new paragraph. Back to Qiime 2 --> :fast_forward: :qiime2: [image] Zhanzhan: I used greegene database: 99_otus.fasta and 99_otu_taxonomy.txt Thank you …

@colinbrislawn :star_struck::star_struck:Thank you for your advice very much！Thanks for your editing! The 99_otus.fasta is 270MB and after extraction and gzip, the 99-v4-ref-seqs.qza is about 8.82MB. The 99_otu_taxonomy.txt is 20.43MB and after importing qiime2, the ref-taxonomy.qza is 2.49MB. And…

Because 99_otus.fasta is only 270MB, I think 2 GB of RAM would be enough... but it looks like you do need more. Could you find a computer with 8 GB and try that? Have you tried using any of the pre-trained classifiers? Colin

@colinbrislawn Thank you Colin! I want to rent a 8GB ram ECS to analyze it and I used a V4 pre-classifier to perform taxonomy annotation and I got the results. But I found no significant differential abundance between two groups. Thank you again for your sincere advice!

Thank you so much! Feel free to open a new thread if you have more questions. Colin

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