diff test-data/tmp/stacks_outputs/populations.log @ 0:bd0bf17caa4d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tmp/stacks_outputs/populations.log	Thu Nov 29 11:38:05 2018 -0500
@@ -0,0 +1,65 @@
+populations v2.2, executed 2018-11-28 13:45:58
+/home/berntm/miniconda3/envs/__stacks@2.2/bin/populations -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 --fstats --fasta_loci --fasta_samples --vcf --genepop --structure --radpainter --plink --phylip --phylip_var --phylip_var_all --fasta_samples_raw
+Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
+populations parameters selected:
+  Percent samples limit per population: 0
+  Locus Population limit: 1
+  Log liklihood filtering: off; threshold: 0
+  Minor allele frequency cutoff: 0
+  Maximum observed heterozygosity cutoff: 1
+  Applying Fst correction: none.
+  Pi/Fis kernel smoothing: off
+  Fstats kernel smoothing: off
+  Bootstrap resampling: off
+
+Parsing population map...
+The population map contained 2 samples, 1 population(s), 1 group(s).
+Working on 2 samples.
+Working on 1 population(s):
+    1: PopA_01, PopA_02
+Working on 1 group(s) of populations:
+    defaultgrp: 1
+
+FASTA consensus sequences for each locus in the metapopulation  will be written to 'stacks_outputs/populations.loci.fa'
+FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples.fa'
+SNPs and calls will be written in VCF format to 'stacks_outputs/populations.snps.vcf'
+Haplotypes will be written in VCF format to 'stacks_outputs/populations.haps.vcf'
+Polymorphic sites in GenePop format will be written to 'stacks_outputs/populations.snps.genepop'
+Polymorphic loci in GenePop format will be written to 'stacks_outputs/populations.haps.genepop'
+Polymorphic sites in Structure format will be written to 'stacks_outputs/populations.structure'
+Polymorphic loci in RADpainter/fineRADstructure format will be written to 'stacks_outputs/populations.haps.radpainter'
+Polymorphic sites in PLINK format will be written to 'stacks_outputs/populations.plink.ped'
+Fixed difference sites in Phylip format will be written to 'stacks_outputs/populations.fixed.phylip'
+   Individual sites written will be logged to 'stacks_outputs/populations.fixed.phylip.log'
+Polymorphic sites in Phylip format will be written to 'stacks_outputs/populations.var.phylip'
+   Individual sites written will be logged to 'stacks_outputs/populations.var.phylip.log'
+Raw FASTA consensus sequences for each sample will be written to 'stacks_outputs/populations.samples-raw.fa'
+Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
+Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
+Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
+Population-level haplotype summary statistics will be written to 'stacks_outputs/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 F-statistics
+  * write the above statistics in the output files
+  * export the genotypes/haplotypes in specified format(s)
+More details in 'stacks_outputs/populations.log.distribs'.
+Now processing...
+Batch 1 
+
+Removed 0 loci that did not pass sample/population constraints from 3 loci.
+Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
+Number of loci with PE contig: 3.00 (100.0%);
+  Mean length of loci: 194.33bp (stderr 0.33);
+Number of loci with SE/PE overlap: 0.00 (0.0%);
+  Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
+Mean genotyped sites per locus: 194.33bp (stderr 0.33).
+
+Population summary statistics (more detail in populations.sumstats_summary.tsv):
+  1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
+
+Population pair divergence statistics (more in populations.fst_summary.tsv and populations.phistats_summary.tsv):
+
+Populations is done.