diff test-data/populations/populations.log @ 0:e5e5617c064a 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/populations/populations.log	Thu Nov 29 11:50:28 2018 -0500
@@ -0,0 +1,43 @@
+populations v2.2, executed 2018-11-27 19:48:37
+/home/berntm/miniconda3/envs/__stacks@2.2/bin/populations -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1
+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
+
+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
+  * 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 282 sites; 0 of those sites were filtered, 2 variant sites remained.
+Mean genotyped sites per locus: 94.00bp (stderr 0.00).
+
+Population summary statistics (more detail in populations.sumstats_summary.tsv):
+  1: 2 samples per locus; pi: 0.66667; all/variant/polymorphic sites: 282/2/2; private alleles: 0
+Populations is done.