Frequently asked questions

How do I start a pipeline using existing basecalls?

Information on how to do this can be found at Starting from existing basecalls.

How do I use Katuali to train a model for medaka?

The Medaka training pipelines section has details on how to accomplish this. The standard config. file template should also act as a guide.

How do I use Katuali with a cluster?

The Submitting tasks to a cluster section has details of how to use Snakemake’s cluster capabilities.

I get an error about not finding libraries. What do I do?

This commonly occurs when using medaka with a GPU e.g.:

ImportError: libcublas.so.9.0: cannot open shared object file: No such file or directory

Setting LD_LIBRARY_PATH in the config should resolve the issue.

Can you implement using X program for performing task Y?

Please feel free to make a feature request on github.