ustacks parameters selected:
  Sample ID: 1
  Min depth of coverage to create a stack: 2
  Max distance allowed between stacks: 2
  Max distance allowed to align secondary reads: 4
  Max number of stacks allowed per de novo locus: 3
  Deleveraging algorithm: disabled
  Removal algorithm: enabled
  Model type: SNP
  Alpha significance level for model: 0.05
  Gapped alignments: disabled
Parsing stacks_inputs/PopA_01.fq
Loading RAD-Tags...done
Loaded 66 RAD-Tags.
  Inserted 7 elements into the RAD-Tags hash map.
  0 reads contained uncalled nucleotides that were modified.
4 initial stacks were populated; 3 stacks were set aside as secondary reads.
Initial coverage mean: 15.75; Std Dev: 7.46241; Max: 27
Deleveraging trigger: 23; Removal trigger: 31
Calculating distance for removing repetitive stacks.
  Distance allowed between stacks: 1; searching with a k-mer length of 47 (48 k-mers per read); 1 k-mer hits required.
Removing repetitive stacks.
  Removed 0 stacks.
  4 stacks remain for merging.
Post-Repeat Removal, coverage depth Mean: 15.75; Std Dev: 7.46241; Max: 27
Calculating distance between stacks...
  Distance allowed between stacks: 2; searching with a k-mer length of 31 (64 k-mers per read); 2 k-mer hits required.
Merging stacks, maximum allowed distance: 2 nucleotide(s)
  4 stacks merged into 3 loci; deleveraged 0 loci; blacklisted 0 loci.
After merging, coverage depth Mean: 21; Std Dev: 4.24264; Max: 27
Merging remainder radtags
  3 remainder sequences left to merge.
  Distance allowed between stacks: 4; searching with a k-mer length of 17 (78 k-mers per read); 10 k-mer hits required.
  Matched 3 remainder reads; unable to match 0 remainder reads.
After remainders merged, coverage depth Mean: 22; Std Dev: 4.32049; Max: 28
Calling final consensus sequences, invoking SNP-calling model...
Number of utilized reads: 66
Writing loci, SNPs, and alleles to 'stacks_outputs/'...
  Refetching sequencing IDs from stacks_inputs/PopA_01.fq... read 66 sequence IDs.
done.
ustacks is done.