I'm trying to use the GMAJ tool on Galaxy, but get this error:
Error loading alignments from bundled file "input.maf": edu.psu.bx.gmaj.BadInputExceptions: Sequence length contradiction" s baboon.1 26891 63 + 1248010 TCAG... Current = 1248010. Previous = 550206
The maf files were extracted using the "Extract MAF blocks" tool, for TBA ENCODE alignments.
The maf data are at http://main.g2.bx.psu.edu/display?id=3054
galaxy-user@lists.galaxyproject.org