Mercurial > repos > pimarin > bakta

annotate test-data/TEST_3/TEST_3.log @ 0:4d315de96666 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
author pimarin
date Wed, 18 May 2022 11:13:45 +0000
parents
children ca9e2125c5de
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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 changeset
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
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
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
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:
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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
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
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
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
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
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
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 changeset
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
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
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 changeset
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
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
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
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 changeset
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
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:
diff changeset
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
parents:
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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:
diff changeset
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
parents:
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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
parents:
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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:
diff changeset
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
parents:
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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
parents:
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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
parents:
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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
parents:
diff changeset
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
parents:
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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:
diff changeset
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
parents:
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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
parents:
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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:
diff changeset
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
parents:
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105 16:56:07.174 - INFO - MAIN - removed tmp dir: /tmp/tmpiur_gfal