Mercurial > repos > pimarin > bakta
comparison test-data/TEST_3/TEST_3.log @ 2:ca9e2125c5de draft
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit fe1cdf884df206d842be4f0768acb06b0bbcf56f"
| author | pimarin |
|---|---|
| date | Wed, 17 Aug 2022 10:29:37 +0000 |
| parents | 4d315de96666 |
| children | eea334d9988b |
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| 1:728e602cd3f7 | 2:ca9e2125c5de |
|---|---|
| 1 parse genome sequences... | 1 parse genome sequences... |
| 2 imported: 2 | 2 imported: 1 |
| 3 filtered & revised: 2 | 3 filtered & revised: 1 |
| 4 plasmids: 1 | 4 plasmids: 1 |
| 5 | 5 |
| 6 start annotation... | 6 start annotation... |
| 7 skip tRNA prediction... | 7 skip tRNA prediction... |
| 8 skip tmRNA prediction... | 8 skip tmRNA prediction... |
| 17 apply feature overlap filters... | 17 apply feature overlap filters... |
| 18 select features and create locus tags... | 18 select features and create locus tags... |
| 19 selected: 0 | 19 selected: 0 |
| 20 | 20 |
| 21 genome statistics: | 21 genome statistics: |
| 22 Genome size: 5,501,884 bp | 22 Genome size: 3,306 bp |
| 23 Contigs/replicons: 2 | 23 Contigs/replicons: 1 |
| 24 GC: 50.5 % | 24 GC: 43.4 % |
| 25 N50: 5,498,578 | 25 N50: 3,306 |
| 26 N ratio: 0.0 % | 26 N ratio: 0.0 % |
| 27 coding density: 0.0 % | 27 coding density: 0.0 % |
| 28 | 28 |
| 29 annotation summary: | 29 annotation summary: |
| 30 tRNAs: 0 | 30 tRNAs: 0 |
| 39 sORFs: 0 | 39 sORFs: 0 |
| 40 gaps: 0 | 40 gaps: 0 |
| 41 oriCs/oriVs: 0 | 41 oriCs/oriVs: 0 |
| 42 oriTs: 0 | 42 oriTs: 0 |
| 43 | 43 |
| 44 export annotation results to: /home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3 | 44 export annotation results to: /tmp/tmpd2jvcl6c/job_working_directory/000/6/working |
| 45 human readable TSV... | 45 human readable TSV... |
| 46 GFF3... | 46 GFF3... |
| 47 INSDC GenBank & EMBL... | 47 INSDC GenBank & EMBL... |
| 48 genome sequences... | 48 genome sequences... |
| 49 feature nucleotide sequences... | 49 feature nucleotide sequences... |
| 51 machine readable JSON... | 51 machine readable JSON... |
| 52 genome and annotation summary... | 52 genome and annotation summary... |
| 53 | 53 |
| 54 If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 | 54 If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 |
| 55 Annotation successfully finished in 0:00 [mm:ss]. | 55 Annotation successfully finished in 0:00 [mm:ss]. |
| 56 CONFIG - prefix=TEST_3 | |
| 57 16:56:06.057 - INFO - CONFIG - output-path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3 | |
| 58 16:56:06.057 - INFO - CONFIG - genus=None | |
| 59 16:56:06.057 - INFO - CONFIG - species=None | |
| 60 16:56:06.057 - INFO - CONFIG - strain=None | |
| 61 16:56:06.057 - INFO - CONFIG - plasmid=None | |
| 62 16:56:06.057 - INFO - CONFIG - complete=False | |
| 63 16:56:06.057 - INFO - CONFIG - prodigal_tf=None | |
| 64 16:56:06.057 - INFO - CONFIG - translation_table=11 | |
| 65 16:56:06.057 - INFO - CONFIG - gram=? | |
| 66 16:56:06.057 - INFO - CONFIG - compliant=False | |
| 67 16:56:06.057 - INFO - CONFIG - locus=None | |
| 68 16:56:06.057 - INFO - CONFIG - locus-tag=None | |
| 69 16:56:06.057 - INFO - CONFIG - keep_contig_headers=False | |
| 70 16:56:06.057 - INFO - CONFIG - replicon-table=None | |
| 71 16:56:06.057 - INFO - CONFIG - skip-tRNA=True | |
| 72 16:56:06.057 - INFO - CONFIG - skip-tmRNA=True | |
| 73 16:56:06.057 - INFO - CONFIG - skip-rRNA=True | |
| 74 16:56:06.057 - INFO - CONFIG - skip-ncRNA=True | |
| 75 16:56:06.057 - INFO - CONFIG - skip-ncRNA-region=True | |
| 76 16:56:06.057 - INFO - CONFIG - skip-CRISPR=True | |
| 77 16:56:06.057 - INFO - CONFIG - skip-CDS=True | |
| 78 16:56:06.058 - INFO - CONFIG - skip-sORF=True | |
| 79 16:56:06.058 - INFO - CONFIG - skip-gap=True | |
| 80 16:56:06.058 - INFO - CONFIG - skip-ori=True | |
| 81 16:56:06.058 - INFO - DB - detected: major=3, minor=0, date=2021-08-9 | |
| 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 | |
| 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 | |
| 84 16:56:06.203 - INFO - MAIN - imported sequences=2 | |
| 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' | |
| 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' | |
| 87 16:56:06.204 - INFO - FASTA - write genome sequences: path=/tmp/tmpiur_gfal/contigs.fna, description=False, wrap=False | |
| 88 16:56:06.220 - INFO - UTILS - generated sequence tag prefix: prefix=BALIOELGAO, length=10, MD5=BA528E50A833FE8DC687CBB0F56A20B6 | |
| 89 16:56:06.220 - INFO - MAIN - selected features=0 | |
| 90 16:56:06.231 - INFO - UTILS - generated sequence tag prefix: prefix=BALIOE, length=6, MD5=BA528E50A833FE8DC687CBB0F56A20B6 | |
| 91 16:56:06.232 - INFO - MAIN - locus tag prefix=BALIOE | |
| 92 16:56:06.232 - INFO - UTILS - genome-size=5501884 | |
| 93 16:56:06.272 - INFO - UTILS - GC=0.505 | |
| 94 16:56:06.272 - INFO - UTILS - N=0.000 | |
| 95 16:56:06.272 - INFO - UTILS - N50=5498578 | |
| 96 16:56:06.273 - INFO - UTILS - coding-ratio=0.000 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 105 16:56:07.174 - INFO - MAIN - removed tmp dir: /tmp/tmpiur_gfal |