Open AdmiralenOla opened 7 years ago
Did you ever find a solution? I'm running into this issue using only 500 genomes.
I never run it with pairwise comparisons; does it work with --no_pairwise? That should tell you whether it is a problem with your input files or with the pairwise comparisons.
Yes it works with --no_pairwise. But that defeats the main purpose of Scoary, which is to control for the population structure, no?
That depends on what you use it for. For my work the --no_pairwise is fine, but I am not hardcore population structure ;)
As originally reported by @dutchscientist in #53 , Scoary currently throws a
when attempting to perform pairwise comparisons on a too big dataset. The exact threshold is unknown to me. I have ran it with ~3500 isolates. This error was reported with ~5800.
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