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

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"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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parse genome sequences...
	imported: 2
	filtered & revised: 2
	plasmids: 1

start annotation...
skip tRNA prediction...
skip tmRNA prediction...
skip rRNA prediction...
skip ncRNA prediction...
skip ncRNA region prediction...
skip CRISPR array prediction...
skip CDS prediction...
skip sORF prediction...
skip gap annotation...
skip oriC/T annotation...
apply feature overlap filters...
select features and create locus tags...
selected: 0

genome statistics:
	Genome size: 5,501,884 bp
	Contigs/replicons: 2
	GC: 50.5 %
	N50: 5,498,578
	N ratio: 0.0 %
	coding density: 0.0 %

annotation summary:
	tRNAs: 0
	tmRNAs: 0
	rRNAs: 0
	ncRNAs: 0
	ncRNA regions: 0
	CRISPR arrays: 0
	CDSs: 0
	  hypotheticals: 0
	  signal peptides: 0
	sORFs: 0
	gaps: 0
	oriCs/oriVs: 0
	oriTs: 0

export annotation results to: /home/pierre/Seafile/ABROMICS/galaxy-tools/tools/bakta/test-data/TEST_3
	human readable TSV...
	GFF3...
	INSDC GenBank & EMBL...
	genome sequences...
	feature nucleotide sequences...
	translated CDS sequences...
	machine readable JSON...
	genome and annotation summary...

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