I was trying to run the taxonomy using the pre-trained classifier.
qiime feature-classifier classify-sklearn
I got the following error
Plugin error from feature-classifier:
Unable to allocate 4.51 GiB for an array with shape (604749824,) and data type float64
Debug info has been saved to /tmp/qiime2-q2cli-err-7l45p5dl.log
How do I overcome this?
@sakshi, I’m pretty sure this is an out of memory error, indicating that your system has insufficient RAM available. Silva is pretty memory- and storage-intensive, so this is a common problem.
- If you’re working in a virtual machine, try increasing the amount of RAM available to the VM.
- If you’re running this command on a supercompute cluster (or similar), try asking the scheduler for more RAM
- If you have access to an institutional cluster but aren’t using it, try running this command there
- If you don’t, but your personal computer doesn’t have enough RAM, you could rent a server and natively install QIIME 2 on that server. Ubuntu servers are pretty straightforward to set up, and this is usually surprisingly cheap.
- If you don’t need silva for your study, you could use a smaller/lighter classifier (like greengenes)
- If none of the above work for you, you could ask a friend with more RAM to run it for you overnight/over the weekend.
- If your friends are all on their computers 24/7, installing more RAM will probably fix the issue. How much RAM will do? I suspect that depends on the size of your data set.
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