TypeError: cannot convert the series to <class 'float'>

[aakashsur]

I'm have a lot of "chromosomes" (genome assembly), and it is causing me to hit this line during zoomify -

cooler/cooler/cli/zoomify.py

Line 197 in d6a7d19

maxres = int(ceil(genome_length / mean_fragsize / HIGLASS_TILE_DIM))

In particular, the previous line seems to result in a series rather than a number -

cooler/cooler/cli/zoomify.py

Line 196 in d6a7d19

mean_fragsize = clr.bins()[['end', 'start']][:].diff(axis=1).mean()

end             NaN
start   -643.747129
dtype: float64

If I understand the code correctly, perhaps a line like this would work -

mean_fragsize = (clr.bins()['end'][:] - clr.bins()['start'][:]).mean()

Then I hit another error -

TypeError: '<' not supported between instances of 'NoneType' and 'int'

Which stems from -

cooler/cooler/reduce.py

Line 462 in d6a7d19

if bases is None:

bases going in was {None} for me, but since a set contain None is True, it goes to the else statement. If I change the if statement to list(bases)[0] it seems to resolve the issue.

And then a final error -

KeyError: "Unable to open object (object '1000' doesn't exist)"

Ultimately I believe this is because my cooler file doesn't have a fixed bin width. Since many contigs were below the lowest bin size (1kb) it probably defaulted to a variable bin size and fails during zoomify.

Here is the output of cooler info

{
    "bin-size": null,
    "bin-type": "variable",
    "creation-date": "2021-08-09T14:32:55.765059",
    "format": "HDF5::Cooler",
    "format-url": "https://github.com/open2c/cooler",
    "format-version": 3,
    "generated-by": "cooler-0.8.11",
    "genome-assembly": "ltarentolae_50000split",
    "nbins": 50061,
    "nchroms": 50061,
    "nnz": 13231173,
    "storage-mode": "symmetric-upper",
    "sum": 30387255
}

Not really sure what the resolution might be, also I don't know if those particular lines are correct per se, but thought I would just point the issue out.

[nvictus]

@aakashsur thank you for reporting this - indeed the issue was with variable bin sizes - and sorry for not getting back sooner. Closing as this was fixed by @Phlya in #332