ERROR: ref genome sequence seems to aligned! remove and restart

[snayfach]

Hello,

When running parsnp v1.2 with the following command: parsnp -r 1339277.3.fna -d genomes -p 1 -o out

I get the following strange error:

-->Reading Genbank file(s) for reference (.gbk) ..
  |->[WARNING]: no genbank file provided for reference annotations, skipping..
ERROR: ref genome sequence 1339277.3.fna seems to aligned! remove and restart

However, if I specify a different genome with -r, the program runs to completion. All genomes are in the genomes directory. All are draft genomes from isolates from the same species.

I'm trying to incorporate parsnp into a pipeline, but this unpredictable error is problematic. Any help would be appreciated.

Thanks, Stephen