Mercurial > repos > matthias > stacks2_tsv2bam
comparison test-data/ustacks/ustacks.log @ 0:99d0b19ef534 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
| author | matthias |
|---|---|
| date | Thu, 29 Nov 2018 11:48:13 -0500 |
| parents | |
| children | 60c1c4d7d2c1 |
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| -1:000000000000 | 0:99d0b19ef534 |
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| 1 ustacks parameters selected: | |
| 2 Input file: 'stacks_inputs/PopA_01.1.fq' | |
| 3 Sample ID: 1 | |
| 4 Min depth of coverage to create a stack (m): 3 | |
| 5 Repeat removal algorithm: enabled | |
| 6 Max distance allowed between stacks (M): 2 | |
| 7 Max distance allowed to align secondary reads: 4 | |
| 8 Max number of stacks allowed per de novo locus: 3 | |
| 9 Deleveraging algorithm: disabled | |
| 10 Gapped assembly: enabled | |
| 11 Minimum alignment length: 0.8 | |
| 12 Model type: SNP | |
| 13 Alpha significance level for model: 0.05 | |
| 14 | |
| 15 Loading RAD-Tags... | |
| 16 | |
| 17 Loaded 66 reads; formed: | |
| 18 4 stacks representing 63 primary reads (95.5%) | |
| 19 3 secondary stacks representing 3 secondary reads (4.5%) | |
| 20 | |
| 21 Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) | |
| 22 Removing repetitive stacks: cov > 39 (mean+3*stdev)... | |
| 23 Blacklisted 0 stacks. | |
| 24 Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) | |
| 25 | |
| 26 Assembling stacks (max. dist. M=2)... | |
| 27 Assembled 4 stacks into 3; blacklisted 0 stacks. | |
| 28 Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%) | |
| 29 | |
| 30 Merging secondary stacks (max. dist. N=4 from consensus)... | |
| 31 Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments. | |
| 32 Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) | |
| 33 | |
| 34 Assembling stacks, allowing for gaps (min. match length 80.0%)... | |
| 35 Assembled 3 stacks into 3 stacks. | |
| 36 Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) | |
| 37 | |
| 38 Merging secondary stacks, allowing for gaps (min. match length 80.0%)... | |
| 39 Merged 0 out of 0 secondary reads (-nan%). | |
| 40 Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) | |
| 41 | |
| 42 Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) | |
| 43 Calling consensus sequences and haplotypes for catalog assembly... | |
| 44 Writing tags, SNPs, and alleles files... | |
| 45 Refetching read IDs...done. | |
| 46 ustacks is done. | |
| 47 ustacks parameters selected: | |
| 48 Input file: 'stacks_inputs/PopA_02.1.fq' | |
| 49 Sample ID: 2 | |
| 50 Min depth of coverage to create a stack (m): 3 | |
| 51 Repeat removal algorithm: enabled | |
| 52 Max distance allowed between stacks (M): 2 | |
| 53 Max distance allowed to align secondary reads: 4 | |
| 54 Max number of stacks allowed per de novo locus: 3 | |
| 55 Deleveraging algorithm: disabled | |
| 56 Gapped assembly: enabled | |
| 57 Minimum alignment length: 0.8 | |
| 58 Model type: SNP | |
| 59 Alpha significance level for model: 0.05 | |
| 60 | |
| 61 Loading RAD-Tags... | |
| 62 | |
| 63 Loaded 60 reads; formed: | |
| 64 4 stacks representing 55 primary reads (91.7%) | |
| 65 5 secondary stacks representing 5 secondary reads (8.3%) | |
| 66 | |
| 67 Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) | |
| 68 Removing repetitive stacks: cov > 42 (mean+3*stdev)... | |
| 69 Blacklisted 0 stacks. | |
| 70 Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) | |
| 71 | |
| 72 Assembling stacks (max. dist. M=2)... | |
| 73 Assembled 4 stacks into 3; blacklisted 0 stacks. | |
| 74 Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%) | |
| 75 | |
| 76 Merging secondary stacks (max. dist. N=4 from consensus)... | |
| 77 Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments. | |
| 78 Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) | |
| 79 | |
| 80 Assembling stacks, allowing for gaps (min. match length 80.0%)... | |
| 81 Assembled 3 stacks into 3 stacks. | |
| 82 Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) | |
| 83 | |
| 84 Merging secondary stacks, allowing for gaps (min. match length 80.0%)... | |
| 85 Merged 0 out of 0 secondary reads (-nan%). | |
| 86 Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) | |
| 87 | |
| 88 Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) | |
| 89 Calling consensus sequences and haplotypes for catalog assembly... | |
| 90 Writing tags, SNPs, and alleles files... | |
| 91 Refetching read IDs...done. | |
| 92 ustacks is done. |