comparison test-data/gstacks/gstacks.log.distribs @ 4:285e1f85c11a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty

3:5421b9528827

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	66	22.000	22.000
PopA_02	3	60	20.000	20.000
END effective_coverages_per_sample

BEGIN phasing_rates_per_sample
sample	n_gts	n_multisnp_hets	n_phased	misphasing_rate
PopA_01	1	1	1	0.000
PopA_02	1	1	1	0.000
END phasing_rates_per_sample

BEGIN clockings
Num. threads: 1
Parallel time: 0.0
Average thread time spent:
     0.0  reading (18.1%)
     0.0  processing (74.5%)
             0.0  counting nucleotides (6.9%)
             0.0  genotyping (5.8%)
             0.0  haplotyping (1.6%)
             0.0  computing consensus (6.6%)
             0.0  building_vcf (48.0%)
     0.0  writing_fa (3.4%)
     0.0  writing_vcf (2.0%)
     0.0  clocking (0.6%)
Total time spent writing vcf: 0.0 (1.9%)
VCFwrite block size: mean=1.0(n=3); max=1
END clockings

4:285e1f85c11a

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 (2.9%)
     0.0  processing (95.7%)
             0.0 pre-alignments block (69.1%)
             0.0  reformatting fw-reads (0.2%)
             0.0  assembling (21.2%)
             0.0  initializing alignments (4.4%)
             0.0  aligning (41.3%)
             0.0  merging read pairs (2.0%)
             0.0 post-alignments block (25.2%)
             0.0  filtering reads (0.0%)
             0.0  counting nucleotides (4.0%)
             0.0  genotyping (1.9%)
             0.0  haplotyping (1.2%)
             0.0  computing consensus (0.1%)
             0.0  building_fa (0.1%)
             0.0  building_vcf (17.8%)
     0.0  writing_fa (0.1%)
     0.0  writing_vcf (1.0%)
     0.0  clocking (0.2%)
Total time spent writing vcf: 0.0 (1.0%)
VCFwrite block size: mean=1.0(n=3); max=1
END clockings