Mercurial > repos > iuc > stacks2_tsv2bam
view test-data/ustacks/ustacks.log @ 0:1b270fc77c81 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2019 10:59:53 -0400 |
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ustacks parameters selected: Input file: 'stacks_inputs/PopA_01.1.fastq' 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. ustacks parameters selected: Input file: 'stacks_inputs/PopA_02.1.fastq' 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.