WARNING: some alignment blocks were overlapping

[aminakur]

I ran maf2synteny on a .maf file produced with Cactus. I thought that .maf files can contain overlapping blocks. Why am I getting this output from maf2synteny and what can I do to fix the problem? P.S. maf2synteny still ran and successfully produced output, but can I trust it given this warning?

	Reading maf file
	Started initial compression

	WARNING: some alignment blocks were overlapping by at most 10144
	It is unexpected and might result into nonsense synteny blocks.
	Please note that this tool currently support alignments
	produced by either Cactus or SibeliaZ.

[mikolmogorov]

This is somewhat unexpected result from Cactus, but could be some kind of borderline case. Cactus have evolved a lot since we developed Ragout, so it is somewhat hard for me to tell if this is an issue here. Unfortunately, the entire alignment + synteny block generation pipeline is not straightforward to set up. My best advice would be to see if the resulting synteny blocks have good coverage (70-90%+).