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vanOosterhoutLab / HybridCheck

HybridCheck, an R package for quickly scripting scans of sequence data for recombination regions.
http://vanOosterhoutLab.github.io/HybridCheck/
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Error with triplet generation #29

Open Swap90 opened 4 years ago

Swap90 commented 4 years ago

Hi,

I am facing an issue while generating triplets. I am using following steps to generate the same. Apologies if I have missed any step.

MyAnalysis <- HC$new("chr6_all.fa_mafft_copy_mafft.fa") Reading in sequence file... Looking for duplicates... Checking length of sequences... Subsetting the informative segregating sites... Finished DNA input... Deciding triplets based on results of Four Taxon Tests. Using tests that are globally significant. Warning message: In fttDescision(ftt, "SIGNIFICANT", TripletCombinations, dna) : No four taxon tests were found to be significant, either none were significant or no test has been performed.

MyAnalysis$setParameters("TripletGeneration", Method = 3L) MyAnalysis$setParameters("SSAnalysis", WindowSize = 200L, StepSize = 1L) MyAnalysis$analyzeSS() Initializing new triplets data. Error in triplets$scanTriplets(tripletSelections, DNA, settings) : No triplets have been prepared yet.