Ok, I’m reasonably convinced (particularly from that
free -m you ran earlier) that you have successfully allocated the amount of memory you think you have to your VM. I only asked for clarification because we get a lot of out of memory issues with VMs where people think the VM has X amount of memory available (usually the amount of RAM they have) when really they’ve only given it access to say 2gigs.
That being said, you are definitely running out of memory available to your VM. The amount of memory it takes to run a classifier can vary significantly, but three samples with around 35 total sequences doesn’t sound like a large amount, so I’m not sure why it would be taking up so much memory.
Would you be able to PM me your data so I can attempt to replicate the command on my machine? Your data is probably just hogging a very large amount of RAM in which case you’ll need to allocate even more to your VM (if you have it available), but it can’t hurt to check and make sure nothing strange is happening.
Additionally, where did you get your classifier from? I can see it’s a silva classifier, but which one in particular? That may also have something to do with your high memory usage.
In the meantime, make sure your VM isn’t running anything in the background that is using a large amount of memory.