Mercurial > repos > pimarin > bakta
comparison test-data/TEST_1/TEST_1.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 | 44fb905481f0 |
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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 |
| 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 combine annotations and mark hypotheticals... | 31 combine annotations and mark hypotheticals... |
| 31 analyze hypothetical proteins: 3 | 32 detect pseudogenes... |
| 33 pseudogene candidates: 0 | |
| 34 found pseudogenes: 0 | |
| 35 analyze hypothetical proteins: 2 | |
| 32 detected Pfam hits: 0 | 36 detected Pfam hits: 0 |
| 33 calculated proteins statistics | 37 calculated proteins statistics |
| 34 revise special cases... | 38 revise special cases... |
| 35 extract sORF... | 39 extract sORF... |
| 36 potential: 52 | 40 potential: 22 |
| 37 discarded due to overlaps: 36 | 41 discarded due to overlaps: 2 |
| 38 discarded spurious: 0 | 42 discarded spurious: 0 |
| 39 detected IPSs: 0 | 43 detected IPSs: 0 |
| 40 found PSCs: 0 | 44 found PSCs: 0 |
| 41 lookup annotations... | 45 lookup annotations... |
| 42 filter and combine annotations... | 46 filter and combine annotations... |
| 47 found: 0 | 51 found: 0 |
| 48 detect oriTs... | 52 detect oriTs... |
| 49 found: 0 | 53 found: 0 |
| 50 apply feature overlap filters... | 54 apply feature overlap filters... |
| 51 select features and create locus tags... | 55 select features and create locus tags... |
| 52 selected: 3 | 56 selected: 2 |
| 53 | 57 |
| 54 genome statistics: | 58 genome statistics: |
| 55 Genome size: 3,306 bp | 59 Genome size: 1,330 bp |
| 56 Contigs/replicons: 1 | 60 Contigs/replicons: 1 |
| 57 GC: 43.4 % | 61 GC: 45.2 % |
| 58 N50: 3,306 | 62 N50: 1,330 |
| 59 N ratio: 0.0 % | 63 N ratio: 0.0 % |
| 60 coding density: 65.2 % | 64 coding density: 62.0 % |
| 61 | 65 |
| 62 annotation summary: | 66 annotation summary: |
| 63 tRNAs: 0 | 67 tRNAs: 0 |
| 64 tmRNAs: 0 | 68 tmRNAs: 0 |
| 65 rRNAs: 0 | 69 rRNAs: 0 |
| 66 ncRNAs: 0 | 70 ncRNAs: 0 |
| 67 ncRNA regions: 0 | 71 ncRNA regions: 0 |
| 68 CRISPR arrays: 0 | 72 CRISPR arrays: 0 |
| 69 CDSs: 3 | 73 CDSs: 2 |
| 70 hypotheticals: 3 | 74 hypotheticals: 2 |
| 75 pseudogenes: 0 | |
| 71 signal peptides: 0 | 76 signal peptides: 0 |
| 72 sORFs: 0 | 77 sORFs: 0 |
| 73 gaps: 0 | 78 gaps: 0 |
| 74 oriCs/oriVs: 0 | 79 oriCs/oriVs: 0 |
| 75 oriTs: 0 | 80 oriTs: 0 |
| 76 | 81 |
| 77 export annotation results to: /tmp/tmpd2jvcl6c/job_working_directory/000/2/working | 82 <<<<<<< HEAD |
| 83 export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/2/working | |
| 84 ======= | |
| 85 export annotation results to: /tmp/tmp4jorszj6/job_working_directory/000/2/working | |
| 86 >>>>>>> 195c8410c (change option for plot) | |
| 78 human readable TSV... | 87 human readable TSV... |
| 79 GFF3... | 88 GFF3... |
| 80 INSDC GenBank & EMBL... | 89 INSDC GenBank & EMBL... |
| 81 genome sequences... | 90 genome sequences... |
| 82 feature nucleotide sequences... | 91 feature nucleotide sequences... |
| 83 translated CDS sequences... | 92 translated CDS sequences... |
| 93 circular genome plot... | |
| 84 hypothetical TSV... | 94 hypothetical TSV... |
| 85 translated hypothetical CDS sequences... | 95 translated hypothetical CDS sequences... |
| 86 machine readable JSON... | 96 machine readable JSON... |
| 87 genome and annotation summary... | 97 genome and annotation summary... |
| 88 | 98 |