Mercurial > repos > pimarin > bakta
diff 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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--- a/test-data/TEST_3/TEST_3.log Wed May 18 11:47:02 2022 +0000 +++ b/test-data/TEST_3/TEST_3.log Wed Aug 17 10:29:37 2022 +0000 @@ -1,6 +1,6 @@ parse genome sequences... - imported: 2 - filtered & revised: 2 + imported: 1 + filtered & revised: 1 plasmids: 1 start annotation... @@ -19,10 +19,10 @@ selected: 0 genome statistics: - Genome size: 5,501,884 bp - Contigs/replicons: 2 - GC: 50.5 % - N50: 5,498,578 + Genome size: 3,306 bp + Contigs/replicons: 1 + GC: 43.4 % + N50: 3,306 N ratio: 0.0 % coding density: 0.0 % @@ -41,7 +41,7 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3 +export annotation results to: /tmp/tmpd2jvcl6c/job_working_directory/000/6/working human readable TSV... GFF3... INSDC GenBank & EMBL... @@ -53,53 +53,3 @@ If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685 Annotation successfully finished in 0:00 [mm:ss]. -CONFIG - prefix=TEST_3 -16:56:06.057 - INFO - CONFIG - output-path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3 -16:56:06.057 - INFO - CONFIG - genus=None -16:56:06.057 - INFO - CONFIG - species=None -16:56:06.057 - INFO - CONFIG - strain=None -16:56:06.057 - INFO - CONFIG - plasmid=None -16:56:06.057 - INFO - CONFIG - complete=False -16:56:06.057 - INFO - CONFIG - prodigal_tf=None -16:56:06.057 - INFO - CONFIG - translation_table=11 -16:56:06.057 - INFO - CONFIG - gram=? -16:56:06.057 - INFO - CONFIG - compliant=False -16:56:06.057 - INFO - CONFIG - locus=None -16:56:06.057 - INFO - CONFIG - locus-tag=None -16:56:06.057 - INFO - CONFIG - keep_contig_headers=False -16:56:06.057 - INFO - CONFIG - replicon-table=None -16:56:06.057 - INFO - CONFIG - skip-tRNA=True -16:56:06.057 - INFO - CONFIG - skip-tmRNA=True -16:56:06.057 - INFO - CONFIG - skip-rRNA=True -16:56:06.057 - INFO - CONFIG - skip-ncRNA=True -16:56:06.057 - INFO - CONFIG - skip-ncRNA-region=True -16:56:06.057 - INFO - CONFIG - skip-CRISPR=True -16:56:06.057 - INFO - CONFIG - skip-CDS=True -16:56:06.058 - INFO - CONFIG - skip-sORF=True -16:56:06.058 - INFO - CONFIG - skip-gap=True -16:56:06.058 - INFO - CONFIG - skip-ori=True -16:56:06.058 - INFO - DB - detected: major=3, minor=0, date=2021-08-9 -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 -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 -16:56:06.203 - INFO - MAIN - imported sequences=2 -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' -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' -16:56:06.204 - INFO - FASTA - write genome sequences: path=/tmp/tmpiur_gfal/contigs.fna, description=False, wrap=False -16:56:06.220 - INFO - UTILS - generated sequence tag prefix: prefix=BALIOELGAO, length=10, MD5=BA528E50A833FE8DC687CBB0F56A20B6 -16:56:06.220 - INFO - MAIN - selected features=0 -16:56:06.231 - INFO - UTILS - generated sequence tag prefix: prefix=BALIOE, length=6, MD5=BA528E50A833FE8DC687CBB0F56A20B6 -16:56:06.232 - INFO - MAIN - locus tag prefix=BALIOE -16:56:06.232 - INFO - UTILS - genome-size=5501884 -16:56:06.272 - INFO - UTILS - GC=0.505 -16:56:06.272 - INFO - UTILS - N=0.000 -16:56:06.272 - INFO - UTILS - N50=5498578 -16:56:06.273 - INFO - UTILS - coding-ratio=0.000 -16:56:06.273 - INFO - TSV - write tsv: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.tsv -16:56:06.273 - INFO - GFF - write GFF3: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.gff3 -16:56:06.297 - INFO - INSDC - write GenBank: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.gbff -16:56:06.576 - INFO - INSDC - write EMBL: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.embl -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 -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 -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 -16:56:07.144 - INFO - JSON - write JSON: path=/home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3/TEST_3.json -16:56:07.174 - INFO - MAIN - removed tmp dir: /tmp/tmpiur_gfal