annotate test-data/gstacks/gstacks.log.distribs @ 2:bd5ff77e2036 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"

# Note: Individual distributions can be extracted using the `stacks-dist-extract` utility.
#       e.g. `stacks-dist-extract gstacks.log.distribs dist_name`

BEGIN effective_coverages_per_sample
# For mean_cov_ns, the coverage at each locus is weighted by the number of
# samples present at that locus (i.e. coverage at shared loci counts more).
sample	n_loci	n_used_fw_reads	mean_cov	mean_cov_ns
PopA_01	3	96	32.000	32.000
PopA_02	3	90	30.000	30.000
END effective_coverages_per_sample

BEGIN phasing_rates_per_sample
sample	n_gts	n_multisnp_hets	n_phased	misphasing_rate
PopA_01	3	2	2	0.000
PopA_02	3	3	3	0.000
END phasing_rates_per_sample

BEGIN clockings
Num. threads: 1
Parallel time: 0.0
Average thread time spent:
     0.0  reading (3.0%)
     0.0  processing (95.7%)
             0.0 pre-alignments block (74.4%)
             0.0  reformatting fw-reads (0.2%)
             0.0  assembling (27.3%)
             0.0  initializing alignments (8.7%)
             0.0  aligning (36.6%)
             0.0  merging read pairs (1.6%)
             0.0 post-alignments block (19.8%)
             0.0  filtering reads (0.0%)
             0.0  counting nucleotides (3.2%)
             0.0  genotyping (1.5%)
             0.0  haplotyping (0.9%)
             0.0  computing consensus (0.1%)
             0.0  building_fa (0.1%)
             0.0  building_vcf (14.0%)
     0.0  writing_fa (0.0%)
     0.0  writing_vcf (0.9%)
     0.0  clocking (0.1%)
Total time spent writing vcf: 0.0 (0.8%)
VCFwrite block size: mean=1.0(n=3); max=1
END clockings