 _____ _____                      _        _   
| ____|__  /_ __   ___  _ __  ___| |_ __ _| |_ 
|  _|   / /| '_ \ / _ \| '_ \/ __| __/ _` | __|
| |___ / /_| |_) | (_) | |_) \__ \ || (_| | |_ 
|_____/____| .__/ \___/| .__/|___/\__\__,_|\__|
           |_|         |_|


Starting EZpopstat run
FASTA        : /home/labadmin/Ezmito/uploaded_jobs/claudio_20260626_172148_593126_0b96575a/Ezpcoa.fasta
Pop map      : /home/labadmin/Ezmito/uploaded_jobs/claudio_20260626_172148_593126_0b96575a/Ezpcoa.popmap.tsv
Outdir       : /home/labadmin/Ezmito/complete_jobs/claudio_20260626_172148_593126_0b96575a

Sequences loaded: 41  |  Raw alignment length: 1225 bp
Alignment check passed: all sequences are 1225 bp
Gap deletion: 1225 / 1225 columns retained
  True gap columns removed: 0
  IUPAC ambiguous chars in alignment: 8 (treated as missing per-position, not per-column)
  removed from all columns where any sequence has a non-ATCG character.
Population map loaded: 41 entries
  Popmap validation passed.
Populations: ['CCI', 'CHA', 'CJO', 'COI', 'MCI', 'RCR']
Group map loaded: 6 population→group entries
  Groups: ['Group1', 'Group2']

Computing per-population statistics ...
  Within-pop stats (H, S, π, Tajima's D): per-population complete deletion (DnaSP)
  AMOVA / FST: global complete deletion + raw Hamming distances (Excoffier 1992)

  Population 'CCI': 3 sequences
    Clean columns for 'CCI': 1225 / 1225 | IUPAC chars: 0 (treated as missing)
  Population 'CHA': 7 sequences
    Clean columns for 'CHA': 1225 / 1225 | IUPAC chars: 0 (treated as missing)
  Population 'CJO': 7 sequences
    Clean columns for 'CJO': 1225 / 1225 | IUPAC chars: 3 (treated as missing)
  Population 'COI': 10 sequences
    Clean columns for 'COI': 1225 / 1225 | IUPAC chars: 0 (treated as missing)
  Population 'MCI': 5 sequences
    Clean columns for 'MCI': 1225 / 1225 | IUPAC chars: 0 (treated as missing)
  Population 'RCR': 9 sequences
    Clean columns for 'RCR': 1225 / 1225 | IUPAC chars: 5 (treated as missing)
Population statistics saved: /home/labadmin/Ezmito/complete_jobs/claudio_20260626_172148_593126_0b96575a/population_statistics.tsv
Haplotype assignments saved: /home/labadmin/Ezmito/complete_jobs/claudio_20260626_172148_593126_0b96575a/haplotype_assignments.tsv
Collapsing to unique haplotypes ...
Collapsed FASTA saved: /home/labadmin/Ezmito/complete_jobs/claudio_20260626_172148_593126_0b96575a/collapsed_haplotypes.fasta  (39 haplotypes)

Computing FST / AMOVA ...
Permutations: 9999
Pairwise FST saved: /home/labadmin/Ezmito/complete_jobs/claudio_20260626_172148_593126_0b96575a/FST_pairwise.tsv
AMOVA summary saved: /home/labadmin/Ezmito/complete_jobs/claudio_20260626_172148_593126_0b96575a/AMOVA_summary.tsv

Total runtime: 26.97 seconds

Citations
---------
If you used this tool, please cite:

- Cucini, C., Leo, C., Iannotti, N., Boschi, S., Brunetti, C., Pons, J., Fanciulli, P.P., Frati, F., Carapelli, A., & Nardi, F. (2021). EZmito: a simple and fast tool for multiple mitogenome analyses. Mitochondrial DNA Part B, 6(3), 1101-1109. https://doi.org/10.1080/23802359.2021.1899865


- Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131(2), 479-491. https://doi.org/10.1093/genetics/131.2.479
- Harris, C. R., Millman, K. J., Van Der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., et al. (2020). Array programming with NumPy. Nature, 585(7825), 357-362.
- McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51-56. https://doi.org/10.25080/Majora-92bf1922-00a
