# HG changeset patch # User pimarin # Date 1674492076 0 # Node ID ed4bc0577be65d1f5c515fbee53105d0502a5bba # Parent 8c7499c6f32aa6e1671cddf6254a34d55509c5cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 274e2f6740711cf7709d44951b9ff70c199d5be7 diff -r 8c7499c6f32a -r ed4bc0577be6 bakta.xml --- a/bakta.xml Mon Jan 23 16:29:03 2023 +0000 +++ b/bakta.xml Mon Jan 23 16:41:16 2023 +0000 @@ -1,6 +1,6 @@ - genome annotation via alignment-free sequence identification + Genome annotation via alignment-free sequence identification macro.xml @@ -11,10 +11,9 @@ 4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code - - - - - @@ -215,18 +207,18 @@ -
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+ + + IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.fna --- a/test-data/TEST_2/TEST_2.fna Mon Jan 23 16:29:03 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ ->NC_002127.1 Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.gbff --- a/test-data/TEST_2/TEST_2.gbff Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_2/TEST_2.gbff Mon Jan 23 16:41:16 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS NC_002127.1 1330 bp DNA circular BCT 16-SEP-2022 +LOCUS NC_002127.1 1330 bp DNA circular BCT 19-DEC-2022 DEFINITION Escherichia coli o157:h7 Sakai plasmid pOSAK1, complete sequence. ACCESSION NC_002127 VERSION NC_002127.1 @@ -7,15 +7,15 @@ ORGANISM Escherichia coli o157:h7 Sakai . COMMENT Annotated with Bakta - Software: v1.5.0 + Software: v1.6.1 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 09/16/2022, 07:32:10 + Annotation Date :: 12/19/2022, 10:20:45 Annotation Pipeline :: Bakta - Annotation Software version :: v1.5.0 + Annotation Software version :: v1.6.1 Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.gff3 --- a/test-data/TEST_2/TEST_2.gff3 Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_2/TEST_2.gff3 Mon Jan 23 16:41:16 2023 +0000 @@ -2,7 +2,7 @@ ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # organism Escherichia coli o157:h7 Sakai # Annotated with Bakta -# Software: v1.5.0 +# Software: v1.6.1 # Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.hypotheticals.faa --- a/test-data/TEST_2/TEST_2.hypotheticals.faa Mon Jan 23 16:29:03 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.hypotheticals.tsv --- a/test-data/TEST_2/TEST_2.hypotheticals.tsv Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_2/TEST_2.hypotheticals.tsv Mon Jan 23 16:41:16 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta v1.5.0, https://github.com/oschwengers/bakta +#Annotated with Bakta v1.6.1, https://github.com/oschwengers/bakta #Database v4.0, https://doi.org/10.5281/zenodo.4247252 #Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs NC_002127.1 413 736 + IHHALP_00005 12.1 10.4 diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.json --- a/test-data/TEST_2/TEST_2.json Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_2/TEST_2.json Mon Jan 23 16:41:16 2023 +0000 @@ -79,11 +79,11 @@ } ], "run": { - "start": "2022-09-16 07:32:09", - "end": "2022-09-16 07:32:10" + "start": "2022-12-19 10:20:43", + "end": "2022-12-19 10:20:45" }, "version": { - "bakta": "1.5.0", + "bakta": "1.6.1", "db": "4.0" } } \ No newline at end of file diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.log --- a/test-data/TEST_2/TEST_2.log Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_2/TEST_2.log Mon Jan 23 16:41:16 2023 +0000 @@ -1,3 +1,4 @@ + parse genome sequences... imported: 1 filtered & revised: 1 @@ -76,17 +77,18 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/4/working +export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/4/working human readable TSV... GFF3... INSDC GenBank & EMBL... genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... hypothetical TSV... translated hypothetical 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]. +Annotation successfully finished in 0:01 [mm:ss]. diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.svg Mon Jan 23 16:41:16 2023 +0000 @@ -0,0 +1,2400 @@ + + + + + + + + + +0 bp + + + + + + + + + + +25 bp + + + + + + + + + + +50 bp + + + + + + + + + + +75 bp + + + + + + + + + + +100 bp + + + + + + + + + + +125 bp + + + + + + + + + + +150 bp + + + + + + + + + + +175 bp + + + + + + + + + + +200 bp + + + + + + + + + + +225 bp + + + + + + + + + + +250 bp + + + + + + + + + + +275 bp + + + + + + + + + + +300 bp + + + + + + + + + + +325 bp + + + + + + + + + + +350 bp + + + + + + + + + + +375 bp + + + + + + + + + + +400 bp + + + + + + + + + + +425 bp + + + + + + + + + + +450 bp + + + + + + + + + + +475 bp + + + + + + + + + + +500 bp + + + + + + + + + + +525 bp + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.tsv --- a/test-data/TEST_2/TEST_2.tsv Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_2/TEST_2.tsv Mon Jan 23 16:41:16 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta (v1.5.0): https://github.com/oschwengers/bakta +#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta #Database (v4.0): https://doi.org/10.5281/zenodo.4247252 #Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs NC_002127.1 cds 413 736 + IHHALP_00005 hypothetical protein diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_2/TEST_2.txt --- a/test-data/TEST_2/TEST_2.txt Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_2/TEST_2.txt Mon Jan 23 16:41:16 2023 +0000 @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.5.0 +Software: v1.6.1 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.embl --- a/test-data/TEST_3/TEST_3.embl Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_3/TEST_3.embl Mon Jan 23 16:41:16 2023 +0000 @@ -8,15 +8,15 @@ OC . XX CC Annotated with Bakta -CC Software: v1.5.0 +CC Software: v1.6.1 CC Database: v4.0 CC DOI: 10.1099/mgen.0.000685 CC URL: github.com/oschwengers/bakta CC CC ##Genome Annotation Summary:## -CC Annotation Date :: 09/16/2022, 07:32:21 +CC Annotation Date :: 12/19/2022, 10:21:03 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.5.0 +CC Annotation Software version :: v1.6.1 CC Annotation Database version :: v4.0 CC CDSs :: 0 CC tRNAs :: 0 diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.faa diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.fna --- a/test-data/TEST_3/TEST_3.fna Mon Jan 23 16:29:03 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ ->contig_1 [completeness=complete] [topology=circular] [gcode=11] -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.gbff --- a/test-data/TEST_3/TEST_3.gbff Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_3/TEST_3.gbff Mon Jan 23 16:41:16 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022 +LOCUS contig_1 1330 bp DNA circular BCT 19-DEC-2022 DEFINITION plasmid unnamed1, complete sequence. ACCESSION contig_1 VERSION contig_1 @@ -7,15 +7,15 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.5.0 + Software: v1.6.1 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 09/16/2022, 07:32:21 + Annotation Date :: 12/19/2022, 10:21:03 Annotation Pipeline :: Bakta - Annotation Software version :: v1.5.0 + Annotation Software version :: v1.6.1 Annotation Database version :: v4.0 CDSs :: 0 tRNAs :: 0 diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.gff3 --- a/test-data/TEST_3/TEST_3.gff3 Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_3/TEST_3.gff3 Mon Jan 23 16:41:16 2023 +0000 @@ -1,7 +1,7 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.5.0 +# Software: v1.6.1 # Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.json --- a/test-data/TEST_3/TEST_3.json Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_3/TEST_3.json Mon Jan 23 16:41:16 2023 +0000 @@ -32,11 +32,11 @@ } ], "run": { - "start": "2022-09-16 07:32:20", - "end": "2022-09-16 07:32:21" + "start": "2022-12-19 10:21:02", + "end": "2022-12-19 10:21:03" }, "version": { - "bakta": "1.5.0", + "bakta": "1.6.1", "db": "4.0" } } \ No newline at end of file diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.log --- a/test-data/TEST_3/TEST_3.log Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_3/TEST_3.log Mon Jan 23 16:41:16 2023 +0000 @@ -1,3 +1,4 @@ + parse genome sequences... imported: 1 filtered & revised: 1 @@ -42,13 +43,14 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/6/working +export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/6/working human readable TSV... GFF3... INSDC GenBank & EMBL... genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... machine readable JSON... genome and annotation summary... diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_3/TEST_3.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.svg Mon Jan 23 16:41:16 2023 +0000 @@ -0,0 +1,2397 @@ + + + + + + + + + +0 bp + + + + + + + + + + +25 bp + + + + + + + + + + +50 bp + + + + + + + + + + +75 bp + + + + + + + + + + +100 bp + + + + + + + + + + +125 bp + + + + + + + + + + +150 bp + + + + + + + + + + +175 bp + + + + + + + + + + +200 bp + + + + + + + + + + +225 bp + + + + + + + + + + +250 bp + + + + + + + + + + +275 bp + + + + + + + + + + +300 bp + + + + + + + + + + +325 bp + + + + + + + + + + +350 bp + + + + + + + + + + +375 bp + + + + + + + + + + +400 bp + + + + + + + + + + +425 bp + + + + + + + + + + +450 bp + + + + + + + + + + +475 bp + + + + + + + + + + +500 bp + + + + + + + + + + +525 bp + + + + + 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8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.embl --- a/test-data/TEST_4/TEST_4.embl Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.embl Mon Jan 23 16:41:16 2023 +0000 @@ -8,15 +8,15 @@ OC . XX CC Annotated with Bakta -CC Software: v1.5.0 +CC Software: v1.6.1 CC Database: v4.0 CC DOI: 10.1099/mgen.0.000685 CC URL: github.com/oschwengers/bakta CC CC ##Genome Annotation Summary:## -CC Annotation Date :: 09/16/2022, 07:32:50 +CC Annotation Date :: 12/19/2022, 10:21:31 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.5.0 +CC Annotation Software version :: v1.6.1 CC Annotation Database version :: v4.0 CC CDSs :: 2 CC tRNAs :: 0 diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.faa --- a/test-data/TEST_4/TEST_4.faa Mon Jan 23 16:29:03 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.fna --- a/test-data/TEST_4/TEST_4.fna Mon Jan 23 16:29:03 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ ->p2 [completeness=complete] [topology=circular] [gcode=4] [plasmid-name=pOSAK1] -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.gbff --- a/test-data/TEST_4/TEST_4.gbff Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.gbff Mon Jan 23 16:41:16 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS p2 1330 bp DNA circular BCT 16-SEP-2022 +LOCUS p2 1330 bp DNA circular BCT 19-DEC-2022 DEFINITION plasmid pOSAK1, complete sequence. ACCESSION p2 VERSION p2 @@ -7,15 +7,15 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.5.0 + Software: v1.6.1 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 09/16/2022, 07:32:50 + Annotation Date :: 12/19/2022, 10:21:31 Annotation Pipeline :: Bakta - Annotation Software version :: v1.5.0 + Annotation Software version :: v1.6.1 Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.gff3 --- a/test-data/TEST_4/TEST_4.gff3 Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.gff3 Mon Jan 23 16:41:16 2023 +0000 @@ -1,7 +1,7 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.5.0 +# Software: v1.6.1 # Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.hypotheticals.faa --- a/test-data/TEST_4/TEST_4.hypotheticals.faa Mon Jan 23 16:29:03 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.hypotheticals.tsv --- a/test-data/TEST_4/TEST_4.hypotheticals.tsv Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.hypotheticals.tsv Mon Jan 23 16:41:16 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta v1.5.0, https://github.com/oschwengers/bakta +#Annotated with Bakta v1.6.1, https://github.com/oschwengers/bakta #Database v4.0, https://doi.org/10.5281/zenodo.4247252 #Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs p2 413 736 + IHHALP_00005 12.1 10.4 diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.json --- a/test-data/TEST_4/TEST_4.json Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.json Mon Jan 23 16:41:16 2023 +0000 @@ -79,11 +79,11 @@ } ], "run": { - "start": "2022-09-16 07:32:48", - "end": "2022-09-16 07:32:50" + "start": "2022-12-19 10:21:29", + "end": "2022-12-19 10:21:31" }, "version": { - "bakta": "1.5.0", + "bakta": "1.6.1", "db": "4.0" } } \ No newline at end of file diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.log --- a/test-data/TEST_4/TEST_4.log Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.log Mon Jan 23 16:41:16 2023 +0000 @@ -1,3 +1,4 @@ + parse genome sequences... imported: 1 filtered & revised: 1 @@ -79,13 +80,14 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/12/working +export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/12/working human readable TSV... GFF3... INSDC GenBank & EMBL... genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... hypothetical TSV... translated hypothetical CDS sequences... machine readable JSON... diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.svg Mon Jan 23 16:41:16 2023 +0000 @@ -0,0 +1,2400 @@ + + + + + + + + + +0 bp + + + + + + + + + + +25 bp + + + + + + + + + + +50 bp + + + + + + + + + + +75 bp + + + + + + + + + + +100 bp + + + + + + + + + + +125 bp + + + + + + + + + + +150 bp + + + + + + + + + + +175 bp + + + + + + + + + + +200 bp + + + + + + + + + + +225 bp + + + + + + + + + + +250 bp + + + + + + + + + + +275 bp + + + + + + + + + + +300 bp + + + + + + + + + + +325 bp + + + + + + + + + + +350 bp + + + + + + + + + + +375 bp + + + + + + + + + + +400 bp + + + + + + + + + + +425 bp + + + + + + + + + + +450 bp + + + + + + + + + + +475 bp + + + + + + + + + + +500 bp + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.tsv --- a/test-data/TEST_4/TEST_4.tsv Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.tsv Mon Jan 23 16:41:16 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta (v1.5.0): https://github.com/oschwengers/bakta +#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta #Database (v4.0): https://doi.org/10.5281/zenodo.4247252 #Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs p2 cds 413 736 + IHHALP_00005 hypothetical protein diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_4/TEST_4.txt --- a/test-data/TEST_4/TEST_4.txt Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_4/TEST_4.txt Mon Jan 23 16:41:16 2023 +0000 @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.5.0 +Software: v1.6.1 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_5/TEST_5.log --- a/test-data/TEST_5/TEST_5.log Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_5/TEST_5.log Mon Jan 23 16:41:16 2023 +0000 @@ -1,3 +1,4 @@ + parse genome sequences... imported: 1 filtered & revised: 1 @@ -42,13 +43,14 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/14/working +export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/14/working human readable TSV... GFF3... INSDC GenBank & EMBL... genome sequences... feature nucleotide sequences... translated CDS sequences... + circular genome plot... machine readable JSON... genome and annotation summary... diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/TEST_5/TEST_5.txt --- a/test-data/TEST_5/TEST_5.txt Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/TEST_5/TEST_5.txt Mon Jan 23 16:41:16 2023 +0000 @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.5.0 +Software: v1.6.1 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta diff -r 8c7499c6f32a -r ed4bc0577be6 test-data/amrfinderplus_database.loc --- a/test-data/amrfinderplus_database.loc Mon Jan 23 16:29:03 2023 +0000 +++ b/test-data/amrfinderplus_database.loc Mon Jan 23 16:41:16 2023 +0000 @@ -4,5 +4,5 @@ # value, name, path # # for example -amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db +amrfinderplus_V3.10_2022-10-11.2 V3.10-2022-10-11.2 ${__HERE__}/amrfinderplus-db/latest +amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db/latest diff -r 8c7499c6f32a -r ed4bc0577be6 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Mon Jan 23 16:29:03 2023 +0000 +++ b/tool_data_table_conf.xml.test Mon Jan 23 16:41:16 2023 +0000 @@ -7,5 +7,6 @@ value, name, path +