Debugging common error messages

Error messages

Some error in brainmapper may come from the cellfinder cell detection algorithm. Please also check the cellfinder error messages section.

OSError: [Errno 24] Too many open files

OSError: [Errno 24] Too many open files

This is likely because your default limits are set too low. To fix this, follow the instructions here. If for any reason you don’t want to or can’t change the system-wide limits, running ulimit -n 60000 before running brainmapper should work. This setting will persist for the present shell session, but will have to be repeated if you open a new terminal.

error: unrecognized arguments

main.py: error: unrecognized arguments: data/dataset1

If what comes after unrecognised arguments looks to be the part of the filepath you entered, after a space, then you should enclose the full path in quotation marks. For example, use "/path/to/my data" not path/to/my data. Otherwise, brainmapper will interpret the path as two inputs, separated by a space.

CommandLineInputError: File path: cannot be found.

brainglobe_utils.general.exceptions.CommandLineInputError: File path: '/media/adam/Storage/brainmapper/data/dataset1' cannot be found.

If you see an error like this, there could be a few possible reasons, e.g.:

• The filepath that you’ve passed to brainmapper does not exist, maybe it’s misspelled, or on a drive that isn’t mounted?

• If the filepath that cannot be found looks to be the part of the filepath you entered, after a space, then you should enclose the full path in quotation marks. (i.e. "/path/to/my data" not path/to/my data) . Otherwise brainmapper will interpret the path as two inputs, separated by a space.)