diff test-data/tmp/stacks_outputs/gstacks.log @ 0:ce90584be117 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/gstacks.log	Thu Nov 29 11:52:48 2018 -0500
@@ -0,0 +1,34 @@
+gstacks v2.2, executed 2018-11-28 13:45:54
+/home/berntm/miniconda3/envs/__stacks@2.2/bin/gstacks -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 --var-alpha 0.05 --gt-alpha 0.05
+Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
+
+Configuration for this run:
+  Input mode: denovo
+  Population map: '/tmp/tmpSlCHrR/files/000/dataset_3.dat'
+  Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
+  Output to: 'stacks_outputs/'
+  Model: marukilow (var_alpha: 0.05, 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 100.3 bp;
+  0 paired-end contigs overlapped the forward region (0.0%)
+    Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
+  Out of 126 paired-end reads in these loci (mean 42.0 reads per locus),
+    126 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.