diff test-data/gstacks/gstacks.log @ 0:d35cb34f2b85 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gstacks/gstacks.log	Mon Jul 01 10:59:14 2019 -0400
@@ -0,0 +1,34 @@
+gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11)
+gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
+
+Configuration for this run:
+  Input mode: denovo
+  Population map: 'denovo_map/popmap_cstacks.tsv'
+  Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
+  Output to: 'stacks_outputs/'
+  Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
+
+Reading BAM headers...
+Processing all loci...
+20%...
+50%...
+100%
+
+Attempted to assemble and align paired-end reads for 3 loci:
+  0 loci had no or almost no paired-end reads (0.0%);
+  0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
+  For the remaining 3 loci (100.0%), a paired-end contig was assembled;
+    Average contig size was 204.3 bp;
+  0 paired-end contigs overlapped the forward region (0.0%)
+    Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
+  Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),
+    252 were successfuly aligned (100.0%);
+  Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).
+
+Genotyped 3 loci:
+  effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
+  mean number of sites per locus: 194.3
+  a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing
+
+gstacks is done.