Mercurial > repos > iuc > stacks2_populations
view test-data/denovo_map/denovo_map.log @ 3:b242deb58952 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 07:32:42 -0400 |
parents | 6fba323a242d |
children | 7b881f5f5ad5 |
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denovo_map.pl version 2.52 started at 2020-03-16 15:39:40 /home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired ustacks ========== Sample 1 of 2 'PopA_01' ---------- ustacks -t fastq -f demultiplexed/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01 ustacks parameters selected: Input file: 'demultiplexed/PopA_01.1.fq' Sample ID: 1 Min depth of coverage to create a stack (m): 3 Repeat removal algorithm: enabled Max distance allowed between stacks (M): 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: disabled Gapped assembly: enabled Minimum alignment length: 0.8 Model type: SNP Alpha significance level for model: 0.05 Loading RAD-Tags... Loaded 66 reads; formed: 4 stacks representing 63 primary reads (95.5%) 3 secondary stacks representing 3 secondary reads (4.5%) Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) Removing repetitive stacks: cov > 39 (mean+3*stdev)... Blacklisted 0 stacks. Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) Assembling stacks (max. dist. M=2)... Assembled 4 stacks into 3; blacklisted 0 stacks. Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%) Merging secondary stacks (max. dist. N=4 from consensus)... Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments. Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) Assembling stacks, allowing for gaps (min. match length 80.0%)... Assembled 3 stacks into 3 stacks. Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) Merging secondary stacks, allowing for gaps (min. match length 80.0%)... Merged 0 out of 0 secondary reads (-nan%). Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) Calling consensus sequences and haplotypes for catalog assembly... Writing tags, SNPs, and alleles files... Refetching read IDs...done. ustacks is done. Sample 2 of 2 'PopA_02' ---------- ustacks -t fastq -f demultiplexed/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02 ustacks parameters selected: Input file: 'demultiplexed/PopA_02.1.fq' Sample ID: 2 Min depth of coverage to create a stack (m): 3 Repeat removal algorithm: enabled Max distance allowed between stacks (M): 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: disabled Gapped assembly: enabled Minimum alignment length: 0.8 Model type: SNP Alpha significance level for model: 0.05 Loading RAD-Tags... Loaded 60 reads; formed: 4 stacks representing 55 primary reads (91.7%) 5 secondary stacks representing 5 secondary reads (8.3%) Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) Removing repetitive stacks: cov > 42 (mean+3*stdev)... Blacklisted 0 stacks. Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) Assembling stacks (max. dist. M=2)... Assembled 4 stacks into 3; blacklisted 0 stacks. Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%) Merging secondary stacks (max. dist. N=4 from consensus)... Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments. Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) Assembling stacks, allowing for gaps (min. match length 80.0%)... Assembled 3 stacks into 3 stacks. Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) Merging secondary stacks, allowing for gaps (min. match length 80.0%)... Merged 0 out of 0 secondary reads (-nan%). Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) Calling consensus sequences and haplotypes for catalog assembly... Writing tags, SNPs, and alleles files... Refetching read IDs...done. ustacks is done. Depths of Coverage for Processed Samples: PopA_01: 22.00x PopA_02: 20.00x cstacks ========== cstacks -M denovo_map/popmap_cstacks.tsv -P stacks_outputs cstacks parameters selected: Loci matched based on sequence identity. Number of mismatches allowed between stacks: 1 Gapped alignments: enabled Constructing catalog from 2 samples. Initializing new catalog... Parsing stacks_outputs/PopA_01.tags.tsv Parsing stacks_outputs/PopA_01.snps.tsv Parsing stacks_outputs/PopA_01.alleles.tsv 3 loci were newly added to the catalog. Processing sample stacks_outputs/PopA_02 [2 of 2] Parsing stacks_outputs/PopA_02.tags.tsv Parsing stacks_outputs/PopA_02.snps.tsv Parsing stacks_outputs/PopA_02.alleles.tsv Searching for sequence matches... 3 loci in the catalog, 184 kmers in the catalog hash. Searching for gapped alignments... Merging matches into catalog... 3 loci were matched to a catalog locus. 0 loci were matched to a catalog locus using gapped alignments. 0 loci were newly added to the catalog. 0 loci matched more than one catalog locus, linking them. 0 linked catalog loci were merged into 0 loci. Writing catalog in directory 'stacks_outputs/'. Final catalog contains 3 loci. cstacks is done. sstacks ========== sstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv Searching for matches by sequence identity... Parsing stacks_outputs/catalog.tags.tsv Parsing stacks_outputs/catalog.snps.tsv Parsing stacks_outputs/catalog.alleles.tsv Populating kmer dictionary for exact matches...done. Populating kmer dictionary for gapped alignments...done. Processing sample 'stacks_outputs/PopA_01' [1 of 2] Parsing stacks_outputs/PopA_01.tags.tsv Parsing stacks_outputs/PopA_01.snps.tsv Parsing stacks_outputs/PopA_01.alleles.tsv Searching for sequence matches... 3 sample loci compared against the catalog containing 3 loci. 3 matching loci, 0 contained no verified haplotypes. 0 loci matched more than one catalog locus and were excluded. 0 loci contained SNPs unaccounted for in the catalog and were excluded. 4 total haplotypes examined from matching loci, 4 verified. Searching for gapped alignments... Out of 3 query loci, 0 gapped alignments attempted. 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified. 0 loci matched no catalog locus; 0 loci matched more than one catalog locus and were excluded. 0 loci contained SNPs unaccounted for in the catalog and were excluded. 0 loci had no verified haplotypes. 0 loci had inconsistent alignments to a catalog locus and were excluded. Outputing to file stacks_outputs/PopA_01.matches.tsv Processing sample 'stacks_outputs/PopA_02' [2 of 2] Parsing stacks_outputs/PopA_02.tags.tsv Parsing stacks_outputs/PopA_02.snps.tsv Parsing stacks_outputs/PopA_02.alleles.tsv Searching for sequence matches... 3 sample loci compared against the catalog containing 3 loci. 3 matching loci, 0 contained no verified haplotypes. 0 loci matched more than one catalog locus and were excluded. 0 loci contained SNPs unaccounted for in the catalog and were excluded. 4 total haplotypes examined from matching loci, 4 verified. Searching for gapped alignments... Out of 3 query loci, 0 gapped alignments attempted. 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified. 0 loci matched no catalog locus; 0 loci matched more than one catalog locus and were excluded. 0 loci contained SNPs unaccounted for in the catalog and were excluded. 0 loci had no verified haplotypes. 0 loci had inconsistent alignments to a catalog locus and were excluded. Outputing to file stacks_outputs/PopA_02.matches.tsv sstacks is done. tsv2bam ========== tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ Logging to 'stacks_outputs/tsv2bam.log'. Configuration for this run: Stacks directory: 'stacks_outputs/' Population map: 'denovo_map/popmap_cstacks.tsv' Num. samples: 2 Paired-end reads directory: 'demultiplexed/' Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'. Loading the catalog... Processing sample 'PopA_01'... Processing sample 'PopA_02'... Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records. Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records. tsv2bam is done. gstacks ========== gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv Logging to 'stacks_outputs/gstacks.log'. Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'. Configuration for this run: Input mode: denovo Population map: 'denovo_map/popmap_cstacks.tsv' Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam' Output to: 'stacks_outputs/' Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05) Reading BAM headers... Processing all loci... 20%... 50%... 100% Attempted to assemble and align paired-end reads for 3 loci: 0 loci had no or almost no paired-end reads (0.0%); 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%); For the remaining 3 loci (100.0%), a paired-end contig was assembled; Average contig size was 204.3 bp; 0 paired-end contigs overlapped the forward region (0.0%) Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan; Out of 252 paired-end reads in these loci (mean 84.0 reads per locus), 252 were successfuly aligned (100.0%); Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci). Genotyped 3 loci: effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x mean number of sites per locus: 194.3 a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing gstacks is done. populations ========== populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv Logging to 'stacks_outputs/populations.log'. Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'. populations parameters selected: Percent samples limit per population: 0 Locus Population limit: 1 Percent samples overall: 0 Minor allele frequency cutoff: 0 Maximum observed heterozygosity cutoff: 1 Applying Fst correction: none. Pi/Fis kernel smoothing: off Fstats kernel smoothing: off Bootstrap resampling: off Parsing population map... The population map contained 2 samples, 1 population(s), 1 group(s). Working on 2 samples. Working on 1 population(s): 1: PopA_01, PopA_02 Working on 1 group(s) of populations: defaultgrp: 1 Raw haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv' Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv' Processing data in batches: * load a batch of catalog loci and apply filters * compute SNP- and haplotype-wise per-population statistics * write the above statistics in the output files * export the genotypes/haplotypes in specified format(s) More details in 'stacks_outputs/populations.log.distribs'. Now processing... Batch 1 Removed 0 loci that did not pass sample/population constraints from 3 loci. Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained. Number of loci with PE contig: 3.00 (100.0%); Mean length of loci: 194.33bp (stderr 0.33); Number of loci with SE/PE overlap: 0.00 (0.0%); Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00); Mean genotyped sites per locus: 194.33bp (stderr 0.33). Population summary statistics (more detail in populations.sumstats_summary.tsv): 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0 Populations is done. denovo_map.pl is done. denovo_map.pl completed at 2020-03-16 15:39:40