After mafStrander the error still happened

[xiangyupan]

Hi,
When I use mafStrander to transfer the strand from "-" to "+" of my maf, there has no error happened. But the output file still has "-" strand block in the reference. The command is as follows:
mafStrander --maf NC_045785.1.maf --seq Balaenoptera_musculus.NC_045785.1 --strand + > NC_045785.1.positive.maf
In the example of mafStrander the parameter "--seq" is hg18 and it will recognize the chr1,chr2,etc. But the reference species in my maf, the name of chromosomes are NC_045785.1,NC_045786.1,NC_045787.1 etc.. Then I try to specify the --seq with Balaenoptera_musculus.NC_045785.1. Some chromosomes go well for the phyloP analysis, but some chromosomes don't.

Hope for any reply.
Best wishes

Pan