before_after.err

Warning messages:
1: In fixXgeno.f2(cross, alleles) :
   --Omitting 1198 male heterozygote genotypes on the X chromosome.
2: In fixXgeno.f2(cross, alleles) :
   --There appear to be some individuals of each cross direction, but "pgm" is not provided.
   Check the X chr genotype data and include a "pgm" column in the phenotype data.
   "pgm" was inferred (probably poorly).
   
3: In summary.cross(cross) :
  Some markers at the same position on chr 1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X; use jittermap().
Warning message:
In matchchr(chr, names(x$geno)) : Chr Y not found
Warning messages:
1: In fixXgeno.f2(cross, alleles) :
   --Omitting 239 male heterozygote genotypes on the X chromosome.
2: In fixXgeno.f2(cross, alleles) :
   --There appear to be some individuals of each cross direction, but "pgm" is not provided.
   Check the X chr genotype data and include a "pgm" column in the phenotype data.
   "pgm" was inferred (probably poorly).
   
3: In summary.cross(cross) :
  Some markers at the same position on chr 1,2,5,6,7,8,9,10,11,12,13,14,15,17,18,19,X; use jittermap().
Warning message:
In est.map(cross = cross_after, error.prob = 0.01) : Didn't converge!
Warning message:
In matchchr(chr, names(x$geno)) : Chr Y not found