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schneebergerlab / findGSE

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.
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Unexpected size of k #4

Closed stefanerb89 closed 10 months ago

stefanerb89 commented 4 years ago

Hello I got this message:

Error in findGSE(histo = args[1], sizek = args[2], outdir = args[3], exp_hom = strtoi(args[4])) : Unexpected size of k: 100. Size k>=15 required. Program exited. Execution halted

The code is

targetsizek     <- sizek
  if(targetsizek  < 15)
  {
    stop(paste("Unexpected size of k: ", targetsizek, ". Size k>=15 required. Program exited.\n",sep=""))
  }

Why I got this error when i choose a size of 100 ?

HeQSun commented 3 years ago

Hi, sorry for the late reply. But have you fixed the problem? It should not exit with larger k's. Did you try other values (while a proper k value can be 17-35 for short reads)?

Best, Hequan