computeMatrix fails with whole chromosome bed (similar to #1114)

[sarjopp]

I am struggling to get computeMatrix to complete. It worked fine with a set of bed files for individual chromosome regions, with 95 single region beds that look like this:
NC_044378.1 29635082 29636878 exon-XM_030623772.1-1 exon ID=exon-XM_030623772.1-1;Parent=rna-XM_030623772.1;Dbxref=GeneID:115696884,Genbank:XM_030623772.1;gbkey=mRNA;gene=LOC115696884;product=cannabidiolic acid synthase-like 1;transcript_id=XM_030623772.1

However, when I provided a single bed for the whole chromosome, I got the error described in issue #1114 (the full set of warnings is pasted below).

I then tried turning the chromosome bed into a "minimal" bed, like so:
NC_044376.1 1009 2371
NC_044376.1 1015003 1015800

But I still got the same error.

File "/home/soppenheim/mendel-nas1/miniconda3/envs/srmp/bin/computeMatrix", line 14, in
main(args)
File "/home/soppenheim/mendel-nas1/miniconda3/envs/srmp/lib/python3.6/site-packages/deeptools/computeMatrix.py", line 421, in main
hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
File "/home/soppenheim/mendel-nas1/miniconda3/envs/srmp/lib/python3.6/site-packages/deeptools/heatmapper.py", line 264, in computeMatrix
verbose=verbose)
File "/home/soppenheim/mendel-nas1/miniconda3/envs/srmp/lib/python3.6/site-packages/deeptools/mapReduce.py", line 142, in mapReduce
res = pool.map_async(func, TASKS).get(9999999)
File "/home/soppenheim/mendel-nas1/miniconda3/envs/srmp/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
multiprocessing.pool.MaybeEncodingError: Error sending result: '[(array([[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
...,
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]]), [['NC_044379.1', [(26913548, 26914154)], 'NC_044379.1:26913548-26914154', 0, '.', '.'], ['NC_044379.1', [(26913548, 26920580)], 'NC_044379.1:26913548-26920580', 0, '.', '.'], ['NC_044379.1', [(26913548, 26920580)], 'NC
_044379.1:26913548-26920580_r1', 0, '.', '.'],
.
.
.
Reason: 'error("'i' format requires -2147483648 <= number <= 2147483647",)'

Can you suggest any solution? I am very frustrated.

Thanks,
Sara