I'm working with GBS data in JoinMap v5. On most of my chromosomes, JoinMap works just fine and gives me a map output. However, on several chromosomes, when I go to construct the map, I get the error "unsuccessful in linkage phase determination error." This error does not appear in the manual and Googling the phrase has not turned up any results.
There are no differences which I can detect in the chromosomes in question. The marker format is identical and there are no issues with incorrectly coded SNP calls. The input data does not include phase information, but this has not been an issue with the other chromosomes.
In the information window following receipt of the error it states:
However, there is only one group, so it cannot be failing to find phasing between groups.
Any help with determining what the error means and how I should go about addressing it would be greatly appreciated.