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

[snayfach]

Looking over the other issues more closely, I noticed this is a duplicate of the open issue #19

A solution to this would be much appreciated

[Ivalize]

Several programs have problems with the contig (I do not know if it happens with parsnp) but most of the time it is better to form pseudo-chromosomes. Also, open the .fna file and check it (looking for symbols or something wrong) or simplify it in the tag name

[romerojazmin]

Has it been a solution or going-around to this issue?