cooler cload pairix on large file halt

[lzlgboy]

I used to generate cool files from pairs.gz file without problem.
There is one .pairs.gz which is 10GB, it neneve finish running and just halt there when the output file is
89M .

I am wondering why this file is never finished? Is it too large?

[nvictus]

It is likely memory related. Could you try increasing the --max-split parameter to 5 or 10 (default is 2)?

[nvictus]

This should be handled somewhat automatically now. There is also an index-free version of cload in v0.7.8 that lets you control memory usage more directly.