Hi all,
I am trying to do phylogenetic analysis using Stacks --phylip option it says no data to write in phylip
Generating nucleotide-level summary statistics for population '1'
Population '1' contained 0 incompatible loci -- more than two alleles present.
Generating nucleotide-level summary statistics for population '2'
Population '2' contained 0 incompatible loci -- more than two alleles present.
Tallying loci across populations...done.
Pruned 264 variant sites due to filter constraints (too many alleles or too few samples at a site, MAF too low, or heterozygosity too high).
Removing 253 additional loci for which all variant sites were filtered... retained 2785 loci.
Regenerating nucleotide-level summary statistics for population '1'
Population '1' contained 0 incompatible loci -- more than two alleles present.
Regenerating nucleotide-level summary statistics for population '2'
Population '2' contained 0 incompatible loci -- more than two alleles present.
Re-tallying loci across populations...done.
Generating haplotype-level summary statistics for population '1'
Generating haplotype-level summary statistics for population '2'
Writing 2785 loci to summary statistics file, './trial/batch_1.sumstats.tsv'
Writing 2785 loci to observed haplotype file, './trial/batch_1.haplotypes.tsv'
Writing population data to Phylip file './trial/batch_1.phylip'; logging nucleotide positions to './trial/batch_1.phylip.log'... No data is available to write to the Phylip file.
Please help
I am trying to do phylogenetic analysis using Stacks --phylip option it says no data to write in phylip
Generating nucleotide-level summary statistics for population '1'
Population '1' contained 0 incompatible loci -- more than two alleles present.
Generating nucleotide-level summary statistics for population '2'
Population '2' contained 0 incompatible loci -- more than two alleles present.
Tallying loci across populations...done.
Pruned 264 variant sites due to filter constraints (too many alleles or too few samples at a site, MAF too low, or heterozygosity too high).
Removing 253 additional loci for which all variant sites were filtered... retained 2785 loci.
Regenerating nucleotide-level summary statistics for population '1'
Population '1' contained 0 incompatible loci -- more than two alleles present.
Regenerating nucleotide-level summary statistics for population '2'
Population '2' contained 0 incompatible loci -- more than two alleles present.
Re-tallying loci across populations...done.
Generating haplotype-level summary statistics for population '1'
Generating haplotype-level summary statistics for population '2'
Writing 2785 loci to summary statistics file, './trial/batch_1.sumstats.tsv'
Writing 2785 loci to observed haplotype file, './trial/batch_1.haplotypes.tsv'
Writing population data to Phylip file './trial/batch_1.phylip'; logging nucleotide positions to './trial/batch_1.phylip.log'... No data is available to write to the Phylip file.
Please help