[MUMmer-help] Mapview Error with GFF Files

[John F W. <jwo...@bi...>]

Hello,

Im trying to use mapview to visualize a nucleotide sequence alignment of
several contigs to a reference with the following command:

mapview -n 1 -f pdf -p $name $name.coords
saccharomyces_cerevisiae_R64-1-1_20110208.gff

with $name representing the prefix used for the delta file and all other
downstream files from the alignment

I receive the following error:
4: FINISHING DATA

  ERROR in the input files ! The reference seq ID can't be found in GFF
files !
      The first column in the GFF file should be the ID of the reference
seq.
      The alignments file should provide the same info in the column before
the last one.

      Here are some example records for the GFF file:

      gnl|FlyBase|X     Dmel3   initial-exon    2155    2413    .       -
    .       X_CG3038.1
      gnl|FlyBase|X     Dmel3   last-exon       1182    2077    .       -
    .       X_CG3038.1
      ...
      The fields are :
      <seq_ID> <source> <exon type> <start> <end> <score> <strand> <frame>
<gene_name>

The Ref entry has the header:
>chrMito

While the GFF entries look like this:
chrMito SGD chromosome 1 85779 . . .
ID=chrMito;dbxref=NCBI:NC_001224;Name=chrMito


GFF file is too large to upload, please contact me directly for gff and
reference file.

Can anyone provide any insight into why it can't find the reference
sequence ID?