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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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nucmer dependency error #46

Closed jacorvar closed 4 years ago

jacorvar commented 4 years ago

Hi,

I have installed KMC and Mummer. They are in the path and work. However, when I try to run seroba, it complains:

ERROR: I tried to get the version of nucmer with: "/apps/mummer/4.0.0.beta2/bin/nucmer --version" and the output didn't match this regular expression: "^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)"

When I run /apps/mummer/4.0.0.beta2/bin/nucmer --version I get 4.0.0beta2, which indeed does not match what sroba expects.

tseemann commented 4 years ago

@jacorvar I think you need mummer 3.x not the much-newer 4.x you are using.