To get consistent behaviour between cactus-align and cactus-pangenome you need to add --pangenome --maxLen 10000 to the former. If you forget the --maxLen part, you get the default of 1000000 which can lead to trouble with big alignments (and why the pangenome setting is short to begin with).
This PR makes fixes it so the default is always 10k for pangenomes whether or not you're running step by step and, of course, adjustable by --maxLen in either case.
I don't want to think about how many hours such a simple issue has cost me while debugging this week...
To get consistent behaviour between
cactus-alignandcactus-pangenomeyou need to add--pangenome --maxLen 10000to the former. If you forget the--maxLenpart, you get the default of1000000which can lead to trouble with big alignments (and why the pangenome setting is short to begin with).This PR makes fixes it so the default is always 10k for pangenomes whether or not you're running step by step and, of course, adjustable by
--maxLenin either case.I don't want to think about how many hours such a simple issue has cost me while debugging this week...