populations v2.52, executed 2020-05-15 22:02:07 (zlib-1.2.11) populations -P /media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/M2_m3/ --popmap /media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/map_Pimelodus_hybrids_SNAPP.txt --out-path /media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/ -p 19 -r 1 -f p_value -t 16 --structure --write-single-snp --phylip --vcf --fasta-loci --phylip-var --phylip-var-all --treemix Locus/sample distributions will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.log.distribs'. populations parameters selected: Percent samples limit per population: 1 Locus Population limit: 19 Percent samples overall: 0 Minor allele frequency cutoff: 0.01 Maximum observed heterozygosity cutoff: 1 Applying Fst correction: P-value correction. Pi/Fis kernel smoothing: off Fstats kernel smoothing: off Bootstrap resampling: off Parsing population map... The population map contained 19 samples, 19 population(s), 1 group(s). Working on 19 samples. Working on 19 population(s): Pcry01_Pgrosskopfii1: Pcry01.fastq Pcry02_Pgrosskopfii2: Pcry02.fastq Pcry04_Pcrypticus1: Pcry04.fastq Pcry05_Pcrypticus2: Pcry05.fastq Pcry07_Pcrypticus3: Pcry07.fastq Pcry06_Pcrypticus4: Pcry06.fastq 78641_Pgrosskopfii3: 78641.fastq 79854_Pyuma1: 79854.fastq 74124_Pgrosskopfii4: 74124.fastq PgaC02_Pgrosskopfii5: PgaCO2.fastq PgaC03_Pgrosskopfii6: PgaCO3.fastq Py14_Pyuma2: Py14.fastq Py15_Pyuma3: Py15.fastq Pim002_Ppictus1: Pim002.fastq Pim003_Ppictus2: Pim003.fastq Pim004_Ppictus3: Pim004.fastq Pbloc03_Pblochii1: Pbloc03.fastq CTGA15742_Pblochii2: CTGA15742l.fastq CTGA12337_Pblochii3: CTGA12337l.fastq Working on 1 group(s) of populations: defaultgrp: Pcry01_Pgrosskopfii1, Pcry02_Pgrosskopfii2, Pcry04_Pcrypticus1, Pcry05_Pcrypticus2, Pcry07_Pcrypticus3, Pcry06_Pcrypticus4, 78641_Pgrosskopfii3, 79854_Pyuma1, 74124_Pgrosskopfii4, PgaCO2_Pgrosskopfii5, PgaCO3_Pgrosskopfii6, Py14_Pyuma2, Py15_Pyuma3, Pim002_Ppictus1, Pim003_Ppictus2, Pim004_Ppictus3, Pbloc03_Pblochii1, CTGA15742_Pblochii2, CTGA12337_Pblochii3 Polymorphic sites in Structure format will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.structure' Fixed difference sites in Phylip format will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.fixed.phylip' SNPs and calls will be written in VCF format to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.snps.vcf' FASTA consensus sequences for each locus in the metapopulation will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.loci.fa' Polymorphic sites in Phylip format will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.var.phylip' All sites (fixed and variable) will be written in Phylip format to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.all.phylip' Per-population SNP allele counts will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.treemix' Raw haplotypes will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.haplotypes.tsv' Population-level summary statistics will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.sumstats.tsv' Population-level haplotype summary statistics will be written to '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.hapstats.tsv' Processing data in batches: * load a batch of catalog loci and apply filters * compute SNP- and haplotype-wise per-population statistics * write the above statistics in the output files * export the genotypes/haplotypes in specified format(s) More details in '/media/salud/TOSHIBAEXT/RADseq_EDNA_pimelodus/TEST1_RADproc_m3_M4/populations.log.distribs'. Now processing... Batch 1 Removed 988422 loci that did not pass sample/population constraints from 992748 loci. Kept 4326 loci, composed of 420654 sites; 257 of those sites were filtered, 999 variant sites remained. Mean genotyped sites per locus: 85bp (stderr 0.10). Population summary statistics (more detail in populations.sumstats_summary.tsv): Pcry01_Pgrosskopfii1: 1 samples per locus; pi: 0.1011; all/variant/polymorphic sites: 420654/999/101; private alleles: 21 Pcry02_Pgrosskopfii2: 1 samples per locus; pi: 0.087087; all/variant/polymorphic sites: 420654/999/87; private alleles: 17 Pcry04_Pcrypticus1: 1 samples per locus; pi: 0.075075; all/variant/polymorphic sites: 420654/999/75; private alleles: 14 Pcry05_Pcrypticus2: 1 samples per locus; pi: 0.074074; all/variant/polymorphic sites: 420654/999/74; private alleles: 16 Pcry07_Pcrypticus3: 1 samples per locus; pi: 0.067067; all/variant/polymorphic sites: 420654/999/67; private alleles: 12 Pcry06_Pcrypticus4: 1 samples per locus; pi: 0.07007; all/variant/polymorphic sites: 420654/999/70; private alleles: 17 78641_Pgrosskopfii3: 1 samples per locus; pi: 0.082082; all/variant/polymorphic sites: 420654/999/82; private alleles: 16 79854_Pyuma1: 1 samples per locus; pi: 0.14214; all/variant/polymorphic sites: 420654/999/142; private alleles: 51 74124_Pgrosskopfii4: 1 samples per locus; pi: 0.074074; all/variant/polymorphic sites: 420654/999/74; private alleles: 15 PgaCO2_Pgrosskopfii5: 1 samples per locus; pi: 0.083083; all/variant/polymorphic sites: 420654/999/83; private alleles: 17 PgaCO3_Pgrosskopfii6: 1 samples per locus; pi: 0.097097; all/variant/polymorphic sites: 420654/999/97; private alleles: 9 Py14_Pyuma2: 1 samples per locus; pi: 0.1011; all/variant/polymorphic sites: 420654/999/101; private alleles: 36 Py15_Pyuma3: 1 samples per locus; pi: 0.1031; all/variant/polymorphic sites: 420654/999/103; private alleles: 37 Pim002_Ppictus1: 1 samples per locus; pi: 0.094094; all/variant/polymorphic sites: 420654/999/94; private alleles: 28 Pim003_Ppictus2: 1 samples per locus; pi: 0.092092; all/variant/polymorphic sites: 420654/999/92; private alleles: 21 Pim004_Ppictus3: 1 samples per locus; pi: 0.095095; all/variant/polymorphic sites: 420654/999/95; private alleles: 21 Pbloc03_Pblochii1: 1 samples per locus; pi: 0.092092; all/variant/polymorphic sites: 420654/999/92; private alleles: 28 CTGA15742_Pblochii2: 1 samples per locus; pi: 0.045045; all/variant/polymorphic sites: 420654/999/45; private alleles: 21 CTGA12337_Pblochii3: 1 samples per locus; pi: 0.092092; all/variant/polymorphic sites: 420654/999/92; private alleles: 25 Populations is done.