Mercurial > repos > iuc > stacks2_refmap
comparison test-data/denovo_map/denovo_map.log @ 2:6dafad990086 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author | iuc |
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date | Thu, 16 Jul 2020 07:26:37 -0400 |
parents | 45385ba40a75 |
children | 5e10f396979e |
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1:319b10947ec1 | 2:6dafad990086 |
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1 denovo_map.pl version 2.4 started at 2019-06-18 10:34:45 | 1 denovo_map.pl version 2.52 started at 2020-03-16 15:39:40 |
2 /home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired | 2 /home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired |
3 | 3 |
4 ustacks | 4 ustacks |
5 ========== | 5 ========== |
6 | 6 |
7 Sample 1 of 2 'PopA_01' | 7 Sample 1 of 2 'PopA_01' |
108 PopA_01: 22.00x | 108 PopA_01: 22.00x |
109 PopA_02: 20.00x | 109 PopA_02: 20.00x |
110 | 110 |
111 cstacks | 111 cstacks |
112 ========== | 112 ========== |
113 cstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv | 113 cstacks -M denovo_map/popmap_cstacks.tsv -P stacks_outputs |
114 | 114 |
115 cstacks parameters selected: | 115 cstacks parameters selected: |
116 Loci matched based on sequence identity. | 116 Loci matched based on sequence identity. |
117 Number of mismatches allowed between stacks: 1 | 117 Number of mismatches allowed between stacks: 1 |
118 Gapped alignments: enabled | 118 Gapped alignments: enabled |
277 Working on 1 population(s): | 277 Working on 1 population(s): |
278 1: PopA_01, PopA_02 | 278 1: PopA_01, PopA_02 |
279 Working on 1 group(s) of populations: | 279 Working on 1 group(s) of populations: |
280 defaultgrp: 1 | 280 defaultgrp: 1 |
281 | 281 |
282 Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv' | 282 Raw haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' |
283 Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' | |
284 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv' | 283 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv' |
285 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv' | 284 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv' |
286 | 285 |
287 Processing data in batches: | 286 Processing data in batches: |
288 * load a batch of catalog loci and apply filters | 287 * load a batch of catalog loci and apply filters |
304 Population summary statistics (more detail in populations.sumstats_summary.tsv): | 303 Population summary statistics (more detail in populations.sumstats_summary.tsv): |
305 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0 | 304 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0 |
306 Populations is done. | 305 Populations is done. |
307 denovo_map.pl is done. | 306 denovo_map.pl is done. |
308 | 307 |
309 denovo_map.pl completed at 2019-06-18 10:34:45 | 308 denovo_map.pl completed at 2020-03-16 15:39:40 |