Mercurial > repos > rdvelazquez > savage

comparison test-data/savage-out1.txt @ 0:0e2450894b69 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/savage commit b'05321082a670b6d41ae9f329b2b54227eecac6ad\n'-dirty
author rdvelazquez
date Fri, 07 Dec 2018 14:30:00 -0500
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-1:000000000000 0:0e2450894b69
1 Mon Nov 26 13:16:47 2018
2
3
4 Input:
5 ../stage_c/singles.fastq
6
7
8 ../contig_overlaps.txt
9
10 Output directory:
11 Maximum number of overlaps: 100000000
12 Threads: 1
13 Minimum clique size: 2
14 Minimal overlap percentage: 0
15 Minimal overlap length: 100
16 Edge threshold: 0.995
17 Overlap threshold (to be reconsidered): 0.9
18 First it: 0
19 Add duplicates: 0
20 Resolve read orientations: 1
21 Keep singletons of length at least: 100
22 Enumerate cliques: 0
23 Error correction: 0
24 Ignore inclusions: 1
25 Graph only: 0
26 FNO: 1
27 Mismatch prob: 0
28 Original readcount: 2200
29 Optimize: 0
30 No inclusion overlaps: 0
31 Merge contigs: 0
32 Remove_multi_occ: 0
33 Remove transitive edges: 1
34 Minimal read length: 100
35 Remove branches: 1
36 Remove backedges: 1
37
38
39 Output:
40 Vertex count: 4
41 Edge count: 2
42 Duplicate overlaps: 0
43 Self-overlaps: 0
44 Inclusions: 0
45 Conflicting edges removed: 0
46 Number of backedges (DFS): 0
47
48 Total clique count: 0
49 Superread (singles) count: 1
50 Superread (paired) count: 0
51 Superread (trivials) count: 2
52 Next overlaps count: 1
53
54 *****************************************
55
56 Mon Nov 26 13:16:47 2018
57
58
59 Input:
60 singles.fastq
61 None
62 None
63 overlaps.txt
64
65 Output directory:
66 Maximum number of overlaps: 100000000
67 Threads: 1
68 Minimum clique size: 2
69 Minimal overlap percentage: 0
70 Minimal overlap length: 100
71 Edge threshold: 0.995
72 Overlap threshold (to be reconsidered): 0.9
73 First it: 0
74 Add duplicates: 0
75 Resolve read orientations: 1
76 Keep singletons of length at least: 100
77 Enumerate cliques: 0
78 Error correction: 0
79 Ignore inclusions: 1
80 Graph only: 0
81 FNO: 1
82 Mismatch prob: 0
83 Original readcount: 2200
84 Optimize: 0
85 No inclusion overlaps: 0
86 Merge contigs: 0
87 Remove_multi_occ: 0
88 Remove transitive edges: 1
89 Minimal read length: 100
90 Remove branches: 1
91 Remove backedges: 1
92
93
94 Output:
95 Vertex count: 3
96 Edge count: 1
97 Duplicate overlaps: 0
98 Self-overlaps: 0
99 Inclusions: 0
100 Conflicting edges removed: 0
101 Number of backedges (DFS): 0
102
103 Total clique count: 0
104 Superread (singles) count: 1
105 Superread (paired) count: 0
106 Superread (trivials) count: 1
107 Next overlaps count: 0
108
109 *****************************************
110