align-families.py stalls on some inputs

[NickSto]

It just hangs at a certain point. It never exits, and the output file never gets any bigger.

This can be a bit of a Heisenbug. It's only been seen on quite large inputs, and stepping through them by giving the script subsets can make it disappear.

Note: It's at least deterministic in that when you run it on the same input twice, you should get the same result. If it worked the first time, it'll work the second time.

Internal notes

First reported by Barbara on 8 Oct 2018. See 2018-10-11 #1

Also reported by Haider on 12 Jan 2022.