Mercurial > repos > pimarin > bakta

comparison test-data/TEST_4/TEST_4.log @ 3:eea334d9988b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 73af464cc860250c3fa3dd433602283ab5a44f53-dirty
author pimarin
date Thu, 22 Dec 2022 15:01:43 +0000
parents ca9e2125c5de
children 8c7499c6f32a
comparison
equal deleted inserted replaced
2:ca9e2125c5de 3:eea334d9988b
1
1 parse genome sequences... 2 parse genome sequences...
2 imported: 1 3 imported: 1
3 filtered & revised: 1 4 filtered & revised: 1
4 plasmids: 1 5 plasmids: 1
5 6
15 predict ncRNA regions... 16 predict ncRNA regions...
16 found: 0 17 found: 0
17 predict CRISPR arrays... 18 predict CRISPR arrays...
18 found: 0 19 found: 0
19 predict & annotate CDSs... 20 predict & annotate CDSs...
20 predicted: 3 21 predicted: 2
21 discarded spurious: 0 22 discarded spurious: 0
22 revised translational exceptions: 0 23 revised translational exceptions: 0
23 detected IPSs: 0 24 detected IPSs: 0
24 found PSCs: 0 25 found PSCs: 0
25 found PSCCs: 0 26 found PSCCs: 0
26 lookup annotations... 27 lookup annotations...
27 conduct expert systems... 28 conduct expert systems...
28 amrfinder: 0 29 amrfinder: 0
29 protein sequences: 0 30 protein sequences: 0
30 user protein sequences: 1 31 user protein sequences: 0
31 combine annotations and mark hypotheticals... 32 combine annotations and mark hypotheticals...
32 analyze hypothetical proteins: 2 33 detect pseudogenes...
34 pseudogene candidates: 0
35 found pseudogenes: 0
36 analyze hypothetical proteins: 2
33 detected Pfam hits: 0 37 detected Pfam hits: 0
34 calculated proteins statistics 38 calculated proteins statistics
35 revise special cases... 39 revise special cases...
36 extract sORF... 40 extract sORF...
37 potential: 41 41 potential: 16
38 discarded due to overlaps: 34 42 discarded due to overlaps: 2
39 discarded spurious: 0 43 discarded spurious: 0
40 detected IPSs: 0 44 detected IPSs: 0
41 found PSCs: 0 45 found PSCs: 0
42 lookup annotations... 46 lookup annotations...
43 filter and combine annotations... 47 filter and combine annotations...
48 found: 0 52 found: 0
49 detect oriTs... 53 detect oriTs...
50 found: 0 54 found: 0
51 apply feature overlap filters... 55 apply feature overlap filters...
52 select features and create locus tags... 56 select features and create locus tags...
53 selected: 3 57 selected: 2
54 58
55 genome statistics: 59 genome statistics:
56 Genome size: 3,306 bp 60 Genome size: 1,330 bp
57 Contigs/replicons: 1 61 Contigs/replicons: 1
58 GC: 43.4 % 62 GC: 45.2 %
59 N50: 3,306 63 N50: 1,330
60 N ratio: 0.0 % 64 N ratio: 0.0 %
61 coding density: 65.2 % 65 coding density: 62.0 %
62 66
63 annotation summary: 67 annotation summary:
64 tRNAs: 0 68 tRNAs: 0
65 tmRNAs: 0 69 tmRNAs: 0
66 rRNAs: 0 70 rRNAs: 0
67 ncRNAs: 0 71 ncRNAs: 0
68 ncRNA regions: 0 72 ncRNA regions: 0
69 CRISPR arrays: 0 73 CRISPR arrays: 0
70 CDSs: 3 74 CDSs: 2
71 hypotheticals: 2 75 hypotheticals: 2
76 pseudogenes: 0
72 signal peptides: 0 77 signal peptides: 0
73 sORFs: 0 78 sORFs: 0
74 gaps: 0 79 gaps: 0
75 oriCs/oriVs: 0 80 oriCs/oriVs: 0
76 oriTs: 0 81 oriTs: 0
77 82
78 export annotation results to: /tmp/tmpd2jvcl6c/job_working_directory/000/12/working 83 export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/12/working
79 human readable TSV... 84 human readable TSV...
80 GFF3... 85 GFF3...
81 INSDC GenBank & EMBL... 86 INSDC GenBank & EMBL...
82 genome sequences... 87 genome sequences...
83 feature nucleotide sequences... 88 feature nucleotide sequences...
84 translated CDS sequences... 89 translated CDS sequences...
90 circular genome plot...
85 hypothetical TSV... 91 hypothetical TSV...
86 translated hypothetical CDS sequences... 92 translated hypothetical CDS sequences...
87 machine readable JSON... 93 machine readable JSON...
88 genome and annotation summary... 94 genome and annotation summary...
89 95