Mercurial > repos > iuc > stacks2_sstacks
diff test-data/gstacks/gstacks.log.distribs @ 0:b7babdb3c219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author | iuc |
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date | Mon, 01 Jul 2019 11:01:59 -0400 |
parents | |
children | 0b8c84a7fdb5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gstacks/gstacks.log.distribs Mon Jul 01 11:01:59 2019 -0400 @@ -0,0 +1,43 @@ +# 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 (3.1%) + 0.0 processing (95.2%) + 0.0 pre-alignments block (72.2%) + 0.0 reformatting fw-reads (0.1%) + 0.0 assembling (22.2%) + 0.0 initializing alignments (5.4%) + 0.0 aligning (42.9%) + 0.0 merging read pairs (1.5%) + 0.0 post-alignments block (21.2%) + 0.0 filtering reads (0.0%) + 0.0 counting nucleotides (3.5%) + 0.0 genotyping (1.9%) + 0.0 haplotyping (1.0%) + 0.0 computing consensus (0.1%) + 0.0 building_fa (0.1%) + 0.0 building_vcf (14.6%) + 0.0 writing_fa (0.1%) + 0.0 writing_vcf (1.3%) + 0.0 clocking (0.2%) +Total time spent writing vcf: 0.0 (1.3%) +VCFwrite block size: mean=1.0(n=3); max=1 +END clockings