Searching for matches by sequence identity...
  Parsing stacks_inputs/catalog.tags.tsv
  Parsing stacks_inputs/catalog.snps.tsv
  Parsing stacks_inputs/catalog.alleles.tsv
Populating kmer dictionary for exact matches...done.
Populating kmer dictionary for gapped alignments...done.

Processing sample 'stacks_inputs/PopA_01' [1 of 2]
  Parsing stacks_inputs/PopA_01.tags.tsv
  Parsing stacks_inputs/PopA_01.snps.tsv
  Parsing stacks_inputs/PopA_01.alleles.tsv
Searching for sequence matches...
3 sample loci compared against the catalog containing 3 loci.
  3 matching loci, 0 contained no verified haplotypes.
  0 loci matched more than one catalog locus and were excluded.
  0 loci contained SNPs unaccounted for in the catalog and were excluded.
  4 total haplotypes examined from matching loci, 4 verified.
Searching for gapped alignments...
Out of 3 query loci, 0 gapped alignments attempted.
  0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
  0 loci matched no catalog locus;
    0 loci matched more than one catalog locus and were excluded.
    0 loci contained SNPs unaccounted for in the catalog and were excluded.
    0 loci had no verified haplotypes.
    0 loci had inconsistent alignments to a catalog locus and were excluded.
Outputing to file stacks_inputs/PopA_01.matches.tsv

Processing sample 'stacks_inputs/PopA_02' [2 of 2]
  Parsing stacks_inputs/PopA_02.tags.tsv
  Parsing stacks_inputs/PopA_02.snps.tsv
  Parsing stacks_inputs/PopA_02.alleles.tsv
Searching for sequence matches...
3 sample loci compared against the catalog containing 3 loci.
  3 matching loci, 0 contained no verified haplotypes.
  0 loci matched more than one catalog locus and were excluded.
  0 loci contained SNPs unaccounted for in the catalog and were excluded.
  4 total haplotypes examined from matching loci, 4 verified.
Searching for gapped alignments...
Out of 3 query loci, 0 gapped alignments attempted.
  0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
  0 loci matched no catalog locus;
    0 loci matched more than one catalog locus and were excluded.
    0 loci contained SNPs unaccounted for in the catalog and were excluded.
    0 loci had no verified haplotypes.
    0 loci had inconsistent alignments to a catalog locus and were excluded.
Outputing to file stacks_inputs/PopA_02.matches.tsv

sstacks is done.