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comparison test-data/denovo_map/denovo_map.log @ 2:d033e1ccb386 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Thu, 16 Jul 2020 07:31:44 -0400
parents 7e5a174bc201
children 8a35a3bc6752
comparison
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1:21d2aa544835 2:d033e1ccb386
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