Troubleshooting

Errors

We've tested these tools internally extensively on different machines and hope that they will work for you out-of-the-box. If not, please follow these guidelines:

First, make sure everything is installed

We've outlined the system installation requirements here.

If you've verified that everything is installed...

Try allocating more memory per core. While we've attempted to make bap2 as memory-friendly as possible, there are still a couple of bottle-neck sections of the code. The majority of the errors that have been encountered by other users have been solved by allocating more memory per core. Please try this.

If you wind up with very few or way too many cells cells...

Check the output plots in the /knee/ directory. While bap2 is written to intelligently detect cutoffs, sometimes these fail when running the tool by default. Examining these knee plots can provide a basis for user-specified cutoffs, which are fully enabled by the command line interface

If all else fails...

Raise a GitHub Issue here and please provide as detailed of information as you can. We will be most responsive and helpful if you are able to provide accurate information about what the error is, what you've tried, and corresponding log files that describe the error.