Error while running Taxonomy classifier

Hello,
I was trying to run the taxonomy using the pre-trained classifier.
qiime feature-classifier classify-sklearn
–i-reads dada2-demux-representative-seqs.qza
–i-classifier silva-138-99-nb-classifier.qza
–o-classification cement-taxonomy
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?

Thanks

@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. :man_shrugging:

Good luck!
Chris :bird:

1 Like