Mercurial > repos > pimarin > bakta
annotate test-data/TEST_3/TEST_3.log @ 0:4d315de96666 draft
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
author | pimarin |
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date | Wed, 18 May 2022 11:13:45 +0000 |
parents | |
children | ca9e2125c5de |
rev | line source |
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0
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
1 parse genome sequences... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
2 imported: 2 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
3 filtered & revised: 2 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
4 plasmids: 1 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
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5 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
6 start annotation... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
7 skip tRNA prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
8 skip tmRNA prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
9 skip rRNA prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
10 skip ncRNA prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
11 skip ncRNA region prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
12 skip CRISPR array prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
13 skip CDS prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
14 skip sORF prediction... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
15 skip gap annotation... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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16 skip oriC/T annotation... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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17 apply feature overlap filters... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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18 select features and create locus tags... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
19 selected: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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20 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
21 genome statistics: |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
22 Genome size: 5,501,884 bp |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
23 Contigs/replicons: 2 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
24 GC: 50.5 % |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
25 N50: 5,498,578 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
26 N ratio: 0.0 % |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
27 coding density: 0.0 % |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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28 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
29 annotation summary: |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
30 tRNAs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
31 tmRNAs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
32 rRNAs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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33 ncRNAs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
34 ncRNA regions: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
35 CRISPR arrays: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
36 CDSs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
37 hypotheticals: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
38 signal peptides: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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39 sORFs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
40 gaps: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
41 oriCs/oriVs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
42 oriTs: 0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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43 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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44 export annotation results to: /home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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45 human readable TSV... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
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46 GFF3... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
47 INSDC GenBank & EMBL... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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48 genome sequences... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
49 feature nucleotide sequences... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
50 translated CDS sequences... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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51 machine readable JSON... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
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52 genome and annotation summary... |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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53 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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54 If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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55 Annotation successfully finished in 0:00 [mm:ss]. |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
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56 CONFIG - prefix=TEST_3 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
57 16:56:06.057 - INFO - CONFIG - output-path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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58 16:56:06.057 - INFO - CONFIG - genus=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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59 16:56:06.057 - INFO - CONFIG - species=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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60 16:56:06.057 - INFO - CONFIG - strain=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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61 16:56:06.057 - INFO - CONFIG - plasmid=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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62 16:56:06.057 - INFO - CONFIG - complete=False |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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63 16:56:06.057 - INFO - CONFIG - prodigal_tf=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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64 16:56:06.057 - INFO - CONFIG - translation_table=11 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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65 16:56:06.057 - INFO - CONFIG - gram=? |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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66 16:56:06.057 - INFO - CONFIG - compliant=False |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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67 16:56:06.057 - INFO - CONFIG - locus=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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68 16:56:06.057 - INFO - CONFIG - locus-tag=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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69 16:56:06.057 - INFO - CONFIG - keep_contig_headers=False |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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70 16:56:06.057 - INFO - CONFIG - replicon-table=None |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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71 16:56:06.057 - INFO - CONFIG - skip-tRNA=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
|
72 16:56:06.057 - INFO - CONFIG - skip-tmRNA=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
diff
changeset
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73 16:56:06.057 - INFO - CONFIG - skip-rRNA=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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74 16:56:06.057 - INFO - CONFIG - skip-ncRNA=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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75 16:56:06.057 - INFO - CONFIG - skip-ncRNA-region=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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76 16:56:06.057 - INFO - CONFIG - skip-CRISPR=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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77 16:56:06.057 - INFO - CONFIG - skip-CDS=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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78 16:56:06.058 - INFO - CONFIG - skip-sORF=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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79 16:56:06.058 - INFO - CONFIG - skip-gap=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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80 16:56:06.058 - INFO - CONFIG - skip-ori=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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81 16:56:06.058 - INFO - DB - detected: major=3, minor=0, date=2021-08-9 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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82 16:56:06.200 - INFO - FASTA - imported: id=NC_002695.2, length=5498578, description=Escherichia coli O157:H7 str. Sakai DNA, complete genome, genomic=True, dna=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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83 16:56:06.203 - INFO - FASTA - imported: id=NC_002127.1, length=3306, description=Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence, genomic=True, dna=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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84 16:56:06.203 - INFO - MAIN - imported sequences=2 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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85 16:56:06.203 - INFO - UTILS - qc: revised sequence: id=contig_1, orig-id=NC_002695.2, type=('contig',), complete=True, topology=circular, name=, description='[completeness=complete] [topology=circular] [gcode=11]', orig-description='Escherichia coli O157:H7 str. Sakai DNA, complete genome' |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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86 16:56:06.204 - INFO - UTILS - qc: revised sequence: id=contig_2, orig-id=NC_002127.1, type=plasmid, complete=True, topology=circular, name=unnamed1, description='[completeness=complete] [topology=circular] [gcode=11]', orig-description='Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence' |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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87 16:56:06.204 - INFO - FASTA - write genome sequences: path=/tmp/tmpiur_gfal/contigs.fna, description=False, wrap=False |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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88 16:56:06.220 - INFO - UTILS - generated sequence tag prefix: prefix=BALIOELGAO, length=10, MD5=BA528E50A833FE8DC687CBB0F56A20B6 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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89 16:56:06.220 - INFO - MAIN - selected features=0 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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90 16:56:06.231 - INFO - UTILS - generated sequence tag prefix: prefix=BALIOE, length=6, MD5=BA528E50A833FE8DC687CBB0F56A20B6 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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91 16:56:06.232 - INFO - MAIN - locus tag prefix=BALIOE |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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92 16:56:06.232 - INFO - UTILS - genome-size=5501884 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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93 16:56:06.272 - INFO - UTILS - GC=0.505 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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94 16:56:06.272 - INFO - UTILS - N=0.000 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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95 16:56:06.272 - INFO - UTILS - N50=5498578 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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96 16:56:06.273 - INFO - UTILS - coding-ratio=0.000 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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97 16:56:06.273 - INFO - TSV - write tsv: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.tsv |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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98 16:56:06.273 - INFO - GFF - write GFF3: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.gff3 |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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99 16:56:06.297 - INFO - INSDC - write GenBank: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.gbff |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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100 16:56:06.576 - INFO - INSDC - write EMBL: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.embl |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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101 16:56:07.100 - INFO - FASTA - write genome sequences: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.fna, description=True, wrap=True |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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102 16:56:07.143 - INFO - FASTA - write feature nucleotide sequences: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.ffn |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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103 16:56:07.144 - INFO - FASTA - write translated CDS/sORF: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.faa |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
parents:
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104 16:56:07.144 - INFO - JSON - write JSON: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.json |
4d315de96666
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
pimarin
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105 16:56:07.174 - INFO - MAIN - removed tmp dir: /tmp/tmpiur_gfal |