Mercurial > repos > pimarin > bakta
diff 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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.log Wed May 18 11:13:45 2022 +0000 @@ -0,0 +1,105 @@ +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