wellington footprints never finishes

[billgreenwald]

Hi!

Whenever I run wellington on my data, I get "waiting on last 80 threads." as the last output

When the process eventually ends, the footprint output file is empty.

any help is appreciated. Thanks!

[jpiper]

Can you try updating to the latest version for me?

[billgreenwald]

I grabbed it off of pip, so if that is not the most up to date version, let me know.

I am getting a new error that the "interval you're trying to footprint is smaller than the parameters you've passed", even when I set -fp to 0,26,2 (ie nothing should be too small). Also, the smallest region in my file is 68 BP, so this shouldnt be an issue.

Some quality of life changes that could make it faster to test and use in the future as well:

• check to see if -h is passed before trying to load the non-flag arguments. The program errors when you give -h without also providing BED, BAM, and output arguments.
• if the output folder doesnt exist, create it for the user instead of returning an error
• give a flag to write to the output folder even if it is full. It takes a while to create, then rm folders, then make them again.
• mention on the README you need python3, not python2