Can't generate coolerfile with cload at very high resolution (200/400bp)

[gdolsten]

Hi, I am having some trouble running cload at higher resolutions (eg 200/400bp). The output freezes at the first batch of chromosomal locations and doesn't continue, even when run for a really long time? How long should it take when running cload pairix and is there anything that can be done to speed it up? Thanks!

[nvictus]

@gdolsten do you remember if this was done with cooler cload pairix and not cooler cload pairs?

We are investigating and suspect the issue with very high-resolution binning and aggregation is due to quirks of Python's multiprocessing that might sometimes get triggered when data chunks reach a certain size. cooler cload pairs does not use multiprocessing and it can be turned off for cload pairix (or the chunksize can be reduced).