comparison test-data/ustacks/ustacks.log @ 0:b9822370f843 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:04:37 -0400
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-1:000000000000 0:b9822370f843
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.