Mercurial > repos > iuc > stacks2_clonefilter
comparison test-data/denovo_map/denovo_map.log @ 2:2f1d464ebfd2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Thu, 16 Jul 2020 07:30:45 -0400 |
| parents | 1b6d07160736 |
| children | e345aadf914f |
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| 1:b75174403a65 | 2:2f1d464ebfd2 |
|---|---|
| 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 |