populations parameters selected: Percent samples limit per population: 0.75 Locus Population limit: 1 Percent samples overall: 0 Minor allele frequency cutoff: 0 Maximum observed heterozygosity cutoff: 1 Applying Fst correction: none. Pi/Fis kernel smoothing: off F-stats kernel smoothing: off Bootstrap resampling: off Parsing population map... The population map contained 96 samples, 12 population(s), 1 group(s). Working on 96 samples. Working on 12 population(s): A: A1, A2, A3, A4, A5, A6, A7, A8 B: B1, B2, B3, B4, B5, B6, B7, B8 C: C1, C2, C3, C4, C5, C6, C7, C8 D: D1, D2, D3, D4, D5, D6, D7, D8 E: E1, E2, E3, E4, E5, E6, E7, E8 F: F1, F2, F3, F4, F5, F6, F7, F8 G: G1, G2, G3, G4, G5, G6, G7, G8 H: H1, H2, H3, H4, H5, H6, H7, H8 I: I1, I2, I3, I4, I5, I6, I7, I8 J: J1, J2, J3, J4, J5, J6, J7, J8 K: K1, K2, K3, K4, K5, K6, K7, K8 L: L1, L2, L3, L4, L5, L6, L7, L8 Working on 1 group(s) of populations: defaultgrp: A, B, C, D, E, F, G, H, I, J, K, L FASTA consensus sequences for each locus in the metapopulation will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.loci.fa' FASTA consensus sequences for each sample will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.samples.fa' SNPs and calls will be written in VCF format to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.snps.vcf' Polymorphic sites in PLINK format will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.plink.ped' Polymorphic sites in HZAR format will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.hzar.csv' Fixed difference sites in Phylip format will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.fixed.phylip' Polymorphic sites in Phylip format will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.var.phylip' Per-population SNP allele counts will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.treemix' Polymorphic sites in GenePop format will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.snps.genepop' Polymorphic sites in Structure format will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.structure' Raw haplotypes will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.haplotypes.tsv' Population-level summary statistics will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.sumstats.tsv' Population-level haplotype summary statistics will be written to '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.hapstats.tsv' Processing data in batches: * load a batch of catalog loci and apply filters * compute SNP- and haplotype-wise per-population statistics * compute SNP- and haplotype-wise deviation from HWE * compute F-statistics * write the above statistics in the output files * export the genotypes/haplotypes in specified format(s) More details in '/data/NGS/NGS01962_Pfosser/R439/Analysis_NGS01962/GBS_analysis/populations/populations.log.distribs'. Now processing... Batch 1 Batch 2 Batch 3 Batch 4 Batch 5 Removed 1262133 loci that did not pass sample/population constraints from 1307980 loci. Kept 45847 loci, composed of 4609215 sites; 31168 of those sites were filtered, 22410 variant sites remained. Mean genotyped sites per locus: 100.53bp (stderr 0.01). Population summary statistics (more detail in populations.sumstats_summary.tsv): A: 6.7636 samples per locus; pi: 0.12372; all/variant/polymorphic sites: 136093/626/201; private alleles: 34 B: 6.5867 samples per locus; pi: 0.18127; all/variant/polymorphic sites: 667395/3327/1694; private alleles: 479 C: 6.8666 samples per locus; pi: 0.11131; all/variant/polymorphic sites: 211127/1027/313; private alleles: 66 D: 6.6205 samples per locus; pi: 0.14427; all/variant/polymorphic sites: 443513/2203/968; private alleles: 314 E: 6.8556 samples per locus; pi: 0.11681; all/variant/polymorphic sites: 267689/1378/463; private alleles: 131 F: 6.5617 samples per locus; pi: 0.11652; all/variant/polymorphic sites: 274279/1403/482; private alleles: 142 G: 6.4081 samples per locus; pi: 0.11994; all/variant/polymorphic sites: 181010/860/281; private alleles: 79 H: 6.8531 samples per locus; pi: 0.11872; all/variant/polymorphic sites: 255345/1300/446; private alleles: 126 I: 6.6833 samples per locus; pi: 0.14521; all/variant/polymorphic sites: 419083/2163/967; private alleles: 334 J: 6.5259 samples per locus; pi: 0.28462; all/variant/polymorphic sites: 3136764/14247/12137; private alleles: 990 K: 6.5554 samples per locus; pi: 0.21147; all/variant/polymorphic sites: 749501/3837/2571; private alleles: 553 L: 6.6156 samples per locus; pi: 0.22516; all/variant/polymorphic sites: 1233302/6507/4310; private alleles: 1090 Number of variable sites found to be significantly out of Hardy-Weinberg equilibrium (<0.05): A: 44 B: 171 C: 59 D: 92 E: 55 F: 48 G: 32 H: 59 I: 81 J: 709 K: 171 L: 434 Number of loci found to be significantly out of Hardy-Weinberg equilibrium (<0.05): A: 635 B: 3321 C: 1044 D: 2027 E: 1396 F: 1364 G: 893 H: 1335 I: 2046 J: 13666 K: 3647 L: 6026 (more detail in populations.sumstats.tsv and populations.hapstats.tsv) Population pair divergence statistics (more in populations.fst_summary.tsv and populations.phistats_summary.tsv): A-B: mean Fst: 0.052821; mean Phi_st: 0.011583; mean Fst': 0.0018657; mean Dxy: 0.0031252 A-C: mean Fst: 0.047116; mean Phi_st: 0.00017522; mean Fst': -0.0055413; mean Dxy: 0.0032023 A-D: mean Fst: 0.049722; mean Phi_st: 0.013447; mean Fst': -0.0025083; mean Dxy: 0.002956 A-E: mean Fst: 0.0526; mean Phi_st: 0.010285; mean Fst': 1.2681e-05; mean Dxy: 0.0030893 A-F: mean Fst: 0.061907; mean Phi_st: 0.024548; mean Fst': 0.010365; mean Dxy: 0.0032735 A-G: mean Fst: 0.10635; mean Phi_st: 0.074409; mean Fst': 0.060347; mean Dxy: 0.0034223 A-H: mean Fst: 0.057243; mean Phi_st: 0.0222; mean Fst': 0.0079511; mean Dxy: 0.0029407 A-I: mean Fst: 0.070415; mean Phi_st: 0.040151; mean Fst': 0.026788; mean Dxy: 0.0028479 A-J: mean Fst: 0.16199; mean Phi_st: 0.17714; mean Fst': 0.12333; mean Dxy: 0.0030808 A-K: mean Fst: 0.15294; mean Phi_st: 0.14986; mean Fst': 0.10769; mean Dxy: 0.003083 A-L: mean Fst: 0.057306; mean Phi_st: 0.025243; mean Fst': 0.0063102; mean Dxy: 0.0029335 B-C: mean Fst: 0.037288; mean Phi_st: -0.0040587; mean Fst': -0.01614; mean Dxy: 0.0027233 B-D: mean Fst: 0.045198; mean Phi_st: 0.0079088; mean Fst': -0.0081214; mean Dxy: 0.0026086 B-E: mean Fst: 0.040162; mean Phi_st: 0.0007633; mean Fst': -0.013058; mean Dxy: 0.0026512 B-F: mean Fst: 0.047576; mean Phi_st: 0.011353; mean Fst': -0.0076956; mean Dxy: 0.0027171 B-G: mean Fst: 0.06779; mean Phi_st: 0.029149; mean Fst': 0.013169; mean Dxy: 0.0031847 B-H: mean Fst: 0.057262; mean Phi_st: 0.026787; mean Fst': 0.0039872; mean Dxy: 0.0025909 B-I: mean Fst: 0.06315; mean Phi_st: 0.032405; mean Fst': 0.010125; mean Dxy: 0.002558 B-J: mean Fst: 0.17483; mean Phi_st: 0.19498; mean Fst': 0.1312; mean Dxy: 0.0032358 B-K: mean Fst: 0.11357; mean Phi_st: 0.11052; mean Fst': 0.065352; mean Dxy: 0.0026753 B-L: mean Fst: 0.070989; mean Phi_st: 0.046608; mean Fst': 0.020598; mean Dxy: 0.002816 C-D: mean Fst: 0.033255; mean Phi_st: -0.013239; mean Fst': -0.021951; mean Dxy: 0.0029341 C-E: mean Fst: 0.027696; mean Phi_st: -0.022012; mean Fst': -0.026602; mean Dxy: 0.002819 C-F: mean Fst: 0.034223; mean Phi_st: -0.011546; mean Fst': -0.019743; mean Dxy: 0.0027977 C-G: mean Fst: 0.090744; mean Phi_st: 0.05636; mean Fst': 0.041254; mean Dxy: 0.003148 C-H: mean Fst: 0.048019; mean Phi_st: 0.0095879; mean Fst': -0.0054939; mean Dxy: 0.0027743 C-I: mean Fst: 0.052983; mean Phi_st: 0.014385; mean Fst': 0.0012872; mean Dxy: 0.002664 C-J: mean Fst: 0.13648; mean Phi_st: 0.14386; mean Fst': 0.088468; mean Dxy: 0.0029286 C-K: mean Fst: 0.11698; mean Phi_st: 0.10628; mean Fst': 0.069233; mean Dxy: 0.0028583 C-L: mean Fst: 0.05138; mean Phi_st: 0.014979; mean Fst': 0.00079729; mean Dxy: 0.0027051 D-E: mean Fst: 0.038082; mean Phi_st: -0.005076; mean Fst': -0.012873; mean Dxy: 0.0027513 D-F: mean Fst: 0.039425; mean Phi_st: -0.0024837; mean Fst': -0.014995; mean Dxy: 0.0028567 D-G: mean Fst: 0.07241; mean Phi_st: 0.035391; mean Fst': 0.021302; mean Dxy: 0.0028549 D-H: mean Fst: 0.049255; mean Phi_st: 0.017661; mean Fst': -0.0048693; mean Dxy: 0.0025791 D-I: mean Fst: 0.055825; mean Phi_st: 0.022139; mean Fst': 0.0021053; mean Dxy: 0.0025466 D-J: mean Fst: 0.16102; mean Phi_st: 0.17357; mean Fst': 0.1153; mean Dxy: 0.0029829 D-K: mean Fst: 0.10598; mean Phi_st: 0.097772; mean Fst': 0.057199; mean Dxy: 0.0026895 D-L: mean Fst: 0.054435; mean Phi_st: 0.023856; mean Fst': 0.0027196; mean Dxy: 0.0026929 E-F: mean Fst: 0.036864; mean Phi_st: -0.0057955; mean Fst': -0.016107; mean Dxy: 0.0027061 E-G: mean Fst: 0.079205; mean Phi_st: 0.046649; mean Fst': 0.029579; mean Dxy: 0.002861 E-H: mean Fst: 0.050037; mean Phi_st: 0.014659; mean Fst': -0.0031286; mean Dxy: 0.0026 E-I: mean Fst: 0.049374; mean Phi_st: 0.0099924; mean Fst': -0.002522; mean Dxy: 0.0025364 E-J: mean Fst: 0.12623; mean Phi_st: 0.13202; mean Fst': 0.078787; mean Dxy: 0.0027156 E-K: mean Fst: 0.11019; mean Phi_st: 0.10475; mean Fst': 0.06095; mean Dxy: 0.0027536 E-L: mean Fst: 0.053047; mean Phi_st: 0.02008; mean Fst': 0.0024511; mean Dxy: 0.002533 F-G: mean Fst: 0.082424; mean Phi_st: 0.048634; mean Fst': 0.029623; mean Dxy: 0.0026907 F-H: mean Fst: 0.060186; mean Phi_st: 0.03129; mean Fst': 0.0062248; mean Dxy: 0.0025388 F-I: mean Fst: 0.05903; mean Phi_st: 0.025946; mean Fst': 0.0054904; mean Dxy: 0.0024649 F-J: mean Fst: 0.13649; mean Phi_st: 0.14477; mean Fst': 0.087966; mean Dxy: 0.0027707 F-K: mean Fst: 0.10361; mean Phi_st: 0.092743; mean Fst': 0.056256; mean Dxy: 0.0025947 F-L: mean Fst: 0.058123; mean Phi_st: 0.027793; mean Fst': 0.0056646; mean Dxy: 0.0025975 G-H: mean Fst: 0.085399; mean Phi_st: 0.057561; mean Fst': 0.035854; mean Dxy: 0.0028064 G-I: mean Fst: 0.066343; mean Phi_st: 0.03497; mean Fst': 0.016127; mean Dxy: 0.0025492 G-J: mean Fst: 0.15131; mean Phi_st: 0.15988; mean Fst': 0.10593; mean Dxy: 0.0028865 G-K: mean Fst: 0.1234; mean Phi_st: 0.11397; mean Fst': 0.073869; mean Dxy: 0.0027854 G-L: mean Fst: 0.077858; mean Phi_st: 0.051455; mean Fst': 0.026469; mean Dxy: 0.002758 H-I: mean Fst: 0.059757; mean Phi_st: 0.025634; mean Fst': 0.0065878; mean Dxy: 0.0027191 H-J: mean Fst: 0.12541; mean Phi_st: 0.12977; mean Fst': 0.07745; mean Dxy: 0.0026471 H-K: mean Fst: 0.10495; mean Phi_st: 0.094375; mean Fst': 0.057294; mean Dxy: 0.0025773 H-L: mean Fst: 0.058917; mean Phi_st: 0.032212; mean Fst': 0.0080157; mean Dxy: 0.0024619 I-J: mean Fst: 0.14397; mean Phi_st: 0.15277; mean Fst': 0.098153; mean Dxy: 0.0028942 I-K: mean Fst: 0.10959; mean Phi_st: 0.10056; mean Fst': 0.059631; mean Dxy: 0.0027699 I-L: mean Fst: 0.066055; mean Phi_st: 0.041361; mean Fst': 0.014579; mean Dxy: 0.0025166 J-K: mean Fst: 0.26983; mean Phi_st: 0.28569; mean Fst': 0.23329; mean Dxy: 0.003849 J-L: mean Fst: 0.20489; mean Phi_st: 0.22849; mean Fst': 0.16405; mean Dxy: 0.0034608 K-L: mean Fst: 0.13806; mean Phi_st: 0.14292; mean Fst': 0.092358; mean Dxy: 0.0028838