Not clear if this is intentional but if running ekidna without the -k option the .vcf file is removed from the output. In the readme it seems to indicate that this output should be kept.
readme example
% ls outdir
ekidna.aln ekidna.fna ekidna.full.aln ekidna.log ekidna.vcf
my output
$ ls no-k
test.aln test.fna test.full.aln test.genome test.log
also produces a .genome file which appears to be just an accession code and genome size.
Not clear if this is intentional but if running ekidna without the -k option the .vcf file is removed from the output. In the readme it seems to indicate that this output should be kept.
readme example % ls outdir ekidna.aln ekidna.fna ekidna.full.aln ekidna.log ekidna.vcf
my output $ ls no-k test.aln test.fna test.full.aln test.genome test.log
also produces a .genome file which appears to be just an accession code and genome size.