Mercurial > repos > iuc > stacks2_refmap
comparison test-data/ustacks/ustacks.log @ 0:45385ba40a75 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author | iuc |
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date | Mon, 01 Jul 2019 11:03:22 -0400 |
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-1:000000000000 | 0:45385ba40a75 |
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1 ustacks parameters selected: | |
2 Input file: 'stacks_inputs/PopA_01.1.fastq' | |
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.fastq' | |
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. |