Mercurial > repos > pimarin > bakta
comparison test-data/TEST_2/TEST_2.log @ 3:eea334d9988b draft
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 |
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| 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 |
| 6 start annotation... | 7 start annotation... |
| 7 predict tRNAs... | 8 skip tRNA prediction... |
| 8 found: 0 | 9 skip tmRNA prediction... |
| 9 predict tmRNAs... | |
| 10 found: 0 | |
| 11 predict rRNAs... | 10 predict rRNAs... |
| 12 found: 0 | 11 found: 0 |
| 13 predict ncRNAs... | 12 predict ncRNAs... |
| 14 found: 0 | 13 found: 0 |
| 15 predict ncRNA regions... | 14 predict ncRNA regions... |
| 16 found: 0 | 15 found: 0 |
| 17 skip CRISPR array prediction... | 16 predict CRISPR arrays... |
| 17 found: 0 | |
| 18 predict & annotate CDSs... | 18 predict & annotate CDSs... |
| 19 predicted: 3 | 19 predicted: 2 |
| 20 discarded spurious: 0 | 20 discarded spurious: 0 |
| 21 revised translational exceptions: 0 | 21 revised translational exceptions: 0 |
| 22 detected IPSs: 0 | 22 detected IPSs: 0 |
| 23 found PSCs: 0 | 23 found PSCs: 0 |
| 24 found PSCCs: 0 | 24 found PSCCs: 0 |
| 25 lookup annotations... | 25 lookup annotations... |
| 26 conduct expert systems... | 26 conduct expert systems... |
| 27 amrfinder: 0 | 27 amrfinder: 0 |
| 28 protein sequences: 0 | 28 protein sequences: 0 |
| 29 combine annotations and mark hypotheticals... | 29 combine annotations and mark hypotheticals... |
| 30 analyze hypothetical proteins: 3 | 30 detect pseudogenes... |
| 31 pseudogene candidates: 0 | |
| 32 found pseudogenes: 0 | |
| 33 analyze hypothetical proteins: 2 | |
| 31 detected Pfam hits: 0 | 34 detected Pfam hits: 0 |
| 32 calculated proteins statistics | 35 calculated proteins statistics |
| 33 revise special cases... | 36 revise special cases... |
| 34 extract sORF... | 37 extract sORF... |
| 35 potential: 52 | 38 potential: 22 |
| 36 discarded due to overlaps: 36 | 39 discarded due to overlaps: 2 |
| 37 discarded spurious: 0 | 40 discarded spurious: 0 |
| 38 detected IPSs: 0 | 41 detected IPSs: 0 |
| 39 found PSCs: 0 | 42 found PSCs: 0 |
| 40 lookup annotations... | 43 lookup annotations... |
| 41 filter and combine annotations... | 44 filter and combine annotations... |
| 42 filtered sORFs: 0 | 45 filtered sORFs: 0 |
| 43 skip gap annotation... | 46 detect gaps... |
| 47 found: 0 | |
| 44 detect oriCs/oriVs... | 48 detect oriCs/oriVs... |
| 45 found: 0 | 49 found: 0 |
| 46 detect oriTs... | 50 detect oriTs... |
| 47 found: 0 | 51 found: 0 |
| 48 apply feature overlap filters... | 52 apply feature overlap filters... |
| 49 select features and create locus tags... | 53 select features and create locus tags... |
| 50 selected: 3 | 54 selected: 2 |
| 51 | 55 |
| 52 genome statistics: | 56 genome statistics: |
| 53 Genome size: 3,306 bp | 57 Genome size: 1,330 bp |
| 54 Contigs/replicons: 1 | 58 Contigs/replicons: 1 |
| 55 GC: 43.4 % | 59 GC: 45.2 % |
| 56 N50: 3,306 | 60 N50: 1,330 |
| 57 N ratio: 0.0 % | 61 N ratio: 0.0 % |
| 58 coding density: 65.2 % | 62 coding density: 62.0 % |
| 59 | 63 |
| 60 annotation summary: | 64 annotation summary: |
| 61 tRNAs: 0 | 65 tRNAs: 0 |
| 62 tmRNAs: 0 | 66 tmRNAs: 0 |
| 63 rRNAs: 0 | 67 rRNAs: 0 |
| 64 ncRNAs: 0 | 68 ncRNAs: 0 |
| 65 ncRNA regions: 0 | 69 ncRNA regions: 0 |
| 66 CRISPR arrays: 0 | 70 CRISPR arrays: 0 |
| 67 CDSs: 3 | 71 CDSs: 2 |
| 68 hypotheticals: 3 | 72 hypotheticals: 2 |
| 73 pseudogenes: 0 | |
| 69 signal peptides: 0 | 74 signal peptides: 0 |
| 70 sORFs: 0 | 75 sORFs: 0 |
| 71 gaps: 0 | 76 gaps: 0 |
| 72 oriCs/oriVs: 0 | 77 oriCs/oriVs: 0 |
| 73 oriTs: 0 | 78 oriTs: 0 |
| 74 | 79 |
| 75 export annotation results to: /tmp/tmpd2jvcl6c/job_working_directory/000/4/working | 80 export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/4/working |
| 76 human readable TSV... | 81 human readable TSV... |
| 77 GFF3... | 82 GFF3... |
| 78 INSDC GenBank & EMBL... | 83 INSDC GenBank & EMBL... |
| 79 genome sequences... | 84 genome sequences... |
| 80 feature nucleotide sequences... | 85 feature nucleotide sequences... |
| 81 translated CDS sequences... | 86 translated CDS sequences... |
| 87 circular genome plot... | |
| 82 hypothetical TSV... | 88 hypothetical TSV... |
| 83 translated hypothetical CDS sequences... | 89 translated hypothetical CDS sequences... |
| 84 machine readable JSON... | 90 machine readable JSON... |
| 85 genome and annotation summary... | 91 genome and annotation summary... |
| 86 | 92 |