ustacks parameters selected:
  Input file: 'stacks_inputs/PopA_01.1.fastq'
  Sample ID: 1
  Min depth of coverage to create a stack (m): 3
  Repeat removal algorithm: enabled
  Max distance allowed between stacks (M): 2
  Max distance allowed to align secondary reads: 4
  Max number of stacks allowed per de novo locus: 3
  Deleveraging algorithm: disabled
  Gapped assembly: enabled
  Minimum alignment length: 0.8
  Model type: SNP
  Alpha significance level for model: 0.05

Loading RAD-Tags...

Loaded 66 reads; formed:
  4 stacks representing 63 primary reads (95.5%)
  3 secondary stacks representing 3 secondary reads (4.5%)

Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
Removing repetitive stacks: cov > 39 (mean+3*stdev)...
  Blacklisted 0 stacks.
Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)

Assembling stacks (max. dist. M=2)...
  Assembled 4 stacks into 3; blacklisted 0 stacks.
Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%)

Merging secondary stacks (max. dist. N=4 from consensus)...
  Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments.
Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)

Assembling stacks, allowing for gaps (min. match length 80.0%)...
  Assembled 3 stacks into 3 stacks.
Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)

Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
  Merged 0 out of 0 secondary reads (-nan%).
Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)

Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
Calling consensus sequences and haplotypes for catalog assembly...
Writing tags, SNPs, and alleles files...
Refetching read IDs...done.
ustacks is done.
ustacks parameters selected:
  Input file: 'stacks_inputs/PopA_02.1.fastq'
  Sample ID: 2
  Min depth of coverage to create a stack (m): 3
  Repeat removal algorithm: enabled
  Max distance allowed between stacks (M): 2
  Max distance allowed to align secondary reads: 4
  Max number of stacks allowed per de novo locus: 3
  Deleveraging algorithm: disabled
  Gapped assembly: enabled
  Minimum alignment length: 0.8
  Model type: SNP
  Alpha significance level for model: 0.05

Loading RAD-Tags...

Loaded 60 reads; formed:
  4 stacks representing 55 primary reads (91.7%)
  5 secondary stacks representing 5 secondary reads (8.3%)

Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
Removing repetitive stacks: cov > 42 (mean+3*stdev)...
  Blacklisted 0 stacks.
Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)

Assembling stacks (max. dist. M=2)...
  Assembled 4 stacks into 3; blacklisted 0 stacks.
Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%)

Merging secondary stacks (max. dist. N=4 from consensus)...
  Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments.
Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)

Assembling stacks, allowing for gaps (min. match length 80.0%)...
  Assembled 3 stacks into 3 stacks.
Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)

Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
  Merged 0 out of 0 secondary reads (-nan%).
Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)

Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
Calling consensus sequences and haplotypes for catalog assembly...
Writing tags, SNPs, and alleles files...
Refetching read IDs...done.
ustacks is done.