Mercurial > repos > iuc > bakta
comparison test-data/TEST_6/TEST_6.log @ 4:3f0aa1b3e816 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
| author | iuc |
|---|---|
| date | Mon, 24 Jul 2023 11:22:16 +0000 |
| parents | |
| children |
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| 3:865ece5ca178 | 4:3f0aa1b3e816 |
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| 1 Bakta v1.8.1 | |
| 2 Options and arguments: | |
| 3 input: /tmp/tmp6wdeee6u/files/4/2/7/dataset_4276a0b6-bcea-42e6-a1e2-9f880300f5a1.dat | |
| 4 db: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/database_path, version 5.0, full | |
| 5 output: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/bakta_output | |
| 6 tmp directory: /tmp/tmp6wdeee6u/tmp/tmpkzvj8z8k | |
| 7 prefix: bakta_output | |
| 8 threads: 1 | |
| 9 translation table: 11 | |
| 10 | |
| 11 parse genome sequences... | |
| 12 imported: 1 | |
| 13 filtered & revised: 1 | |
| 14 plasmids: 1 | |
| 15 | |
| 16 start annotation... | |
| 17 predict tRNAs... | |
| 18 found: 0 | |
| 19 predict tmRNAs... | |
| 20 found: 0 | |
| 21 predict rRNAs... | |
| 22 found: 0 | |
| 23 predict ncRNAs... | |
| 24 found: 0 | |
| 25 predict ncRNA regions... | |
| 26 found: 0 | |
| 27 predict CRISPR arrays... | |
| 28 found: 0 | |
| 29 predict & annotate CDSs... | |
| 30 predicted: 2 | |
| 31 discarded spurious: 0 | |
| 32 revised translational exceptions: 0 | |
| 33 detected IPSs: 0 | |
| 34 found PSCs: 0 | |
| 35 found PSCCs: 0 | |
| 36 lookup annotations... | |
| 37 conduct expert systems... | |
| 38 amrfinder: 0 | |
| 39 protein sequences: 0 | |
| 40 combine annotations and mark hypotheticals... | |
| 41 detect pseudogenes... | |
| 42 pseudogene candidates: 0 | |
| 43 found pseudogenes: 0 | |
| 44 analyze hypothetical proteins: 2 | |
| 45 detected Pfam hits: 0 | |
| 46 calculated proteins statistics | |
| 47 revise special cases... | |
| 48 extract sORF... | |
| 49 potential: 22 | |
| 50 discarded due to overlaps: 2 | |
| 51 discarded spurious: 0 | |
| 52 detected IPSs: 0 | |
| 53 found PSCs: 0 | |
| 54 lookup annotations... | |
| 55 filter and combine annotations... | |
| 56 filtered sORFs: 0 | |
| 57 detect gaps... | |
| 58 found: 0 | |
| 59 detect oriCs/oriVs... | |
| 60 found: 0 | |
| 61 detect oriTs... | |
| 62 found: 0 | |
| 63 apply feature overlap filters... | |
| 64 select features and create locus tags... | |
| 65 selected: 2 | |
| 66 improve annotations... | |
| 67 revised gene symbols: 0 | |
| 68 | |
| 69 genome statistics: | |
| 70 Genome size: 1,330 bp | |
| 71 Contigs/replicons: 1 | |
| 72 GC: 45.2 % | |
| 73 N50: 1,330 | |
| 74 N ratio: 0.0 % | |
| 75 coding density: 62.0 % | |
| 76 | |
| 77 annotation summary: | |
| 78 tRNAs: 0 | |
| 79 tmRNAs: 0 | |
| 80 rRNAs: 0 | |
| 81 ncRNAs: 0 | |
| 82 ncRNA regions: 0 | |
| 83 CRISPR arrays: 0 | |
| 84 CDSs: 2 | |
| 85 hypotheticals: 2 | |
| 86 pseudogenes: 0 | |
| 87 signal peptides: 0 | |
| 88 sORFs: 0 | |
| 89 gaps: 0 | |
| 90 oriCs/oriVs: 0 | |
| 91 oriTs: 0 | |
| 92 | |
| 93 export annotation results to: /tmp/tmp6wdeee6u/job_working_directory/000/15/working/bakta_output | |
| 94 human readable TSV... | |
| 95 GFF3... | |
| 96 INSDC GenBank & EMBL... | |
| 97 genome sequences... | |
| 98 feature nucleotide sequences... | |
| 99 translated CDS sequences... | |
| 100 circular genome plot... | |
| 101 hypothetical TSV... | |
| 102 translated hypothetical CDS sequences... | |
| 103 machine readable JSON... | |
| 104 genome and annotation summary... | |
| 105 | |
| 106 If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 | |
| 107 Annotation successfully finished in 0:01 [mm:ss]. |