# HG changeset patch # User pimarin # Date 1674491343 0 # Node ID 8c7499c6f32aa6e1671cddf6254a34d55509c5cc # Parent c75629db91ff5e28935647a83c98d6c695d6b980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5e03f5cfb2216af80ad3ca499504ebdb92ade2c5 diff -r c75629db91ff -r 8c7499c6f32a bakta.xml --- a/bakta.xml Mon Jan 23 14:05:58 2023 +0000 +++ b/bakta.xml Mon Jan 23 16:29:03 2023 +0000 @@ -1,6 +1,6 @@ - Genome annotation via alignment-free sequence identification + genome annotation via alignment-free sequence identification macro.xml @@ -11,9 +11,10 @@ 4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code + + + + + @@ -207,18 +215,18 @@ -

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+ + + 1.6.1 - 1.6.1 - 1.6.1 1.5 0 21.05 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.embl --- a/test-data/TEST_1/TEST_1.embl Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.embl Mon Jan 23 16:29:03 2023 +0000 @@ -8,15 +8,15 @@ OC . XX CC Annotated with Bakta -CC Software: v1.6.1 +CC Software: v1.5.0 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 :: 01/03/2023, 10:02:08 +CC Annotation Date :: 09/16/2022, 07:31:59 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.6.1 +CC Annotation Software version :: v1.5.0 CC Annotation Database version :: v4.0 CC CDSs :: 2 CC tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.gbff --- a/test-data/TEST_1/TEST_1.gbff Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.gbff Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS contig_1 1330 bp DNA circular BCT 03-JAN-2023 +LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022 DEFINITION plasmid unnamed1, complete sequence. ACCESSION contig_1 VERSION contig_1 @@ -7,15 +7,15 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.6.1 + Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 01/03/2023, 10:02:08 + Annotation Date :: 09/16/2022, 07:31:59 Annotation Pipeline :: Bakta - Annotation Software version :: v1.6.1 + Annotation Software version :: v1.5.0 Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.gff3 --- a/test-data/TEST_1/TEST_1.gff3 Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.gff3 Mon Jan 23 16:29:03 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: v1.6.1 +# Software: v1.5.0 # Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.hypotheticals.tsv --- a/test-data/TEST_1/TEST_1.hypotheticals.tsv Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta v1.6.1, https://github.com/oschwengers/bakta +#Annotated with Bakta v1.5.0, 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 contig_1 413 736 + IHHALP_00005 12.1 10.4 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.json --- a/test-data/TEST_1/TEST_1.json Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.json Mon Jan 23 16:29:03 2023 +0000 @@ -80,11 +80,11 @@ } ], "run": { - "start": "2023-01-03 10:02:07", - "end": "2023-01-03 10:02:08" + "start": "2022-09-16 07:31:58", + "end": "2022-09-16 07:31:59" }, "version": { - "bakta": "1.6.1", + "bakta": "1.5.0", "db": "4.0" } } \ No newline at end of file diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.log --- a/test-data/TEST_1/TEST_1.log Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.log Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,3 @@ - parse genome sequences... imported: 1 filtered & revised: 1 @@ -79,14 +78,13 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/2/working +export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/2/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 c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.tsv --- a/test-data/TEST_1/TEST_1.tsv Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.tsv Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta +#Annotated with Bakta (v1.5.0): 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 contig_1 cds 413 736 + IHHALP_00005 hypothetical protein diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_1/TEST_1.txt --- a/test-data/TEST_1/TEST_1.txt Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_1/TEST_1.txt Mon Jan 23 16:29:03 2023 +0000 @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.6.1 +Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.embl --- a/test-data/TEST_2/TEST_2.embl Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.embl Mon Jan 23 16:29:03 2023 +0000 @@ -8,15 +8,15 @@ OC . XX CC Annotated with Bakta -CC Software: v1.6.1 +CC Software: v1.5.0 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 :: 12/19/2022, 10:20:45 +CC Annotation Date :: 09/16/2022, 07:32:10 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.6.1 +CC Annotation Software version :: v1.5.0 CC Annotation Database version :: v4.0 CC CDSs :: 2 CC tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.faa Mon Jan 23 16:29:03 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.fna Mon Jan 23 16:29:03 2023 +0000 @@ -0,0 +1,24 @@ +>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 c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.gbff --- a/test-data/TEST_2/TEST_2.gbff Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.gbff Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS NC_002127.1 1330 bp DNA circular BCT 19-DEC-2022 +LOCUS NC_002127.1 1330 bp DNA circular BCT 16-SEP-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: v1.6.1 + Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 12/19/2022, 10:20:45 + Annotation Date :: 09/16/2022, 07:32:10 Annotation Pipeline :: Bakta - Annotation Software version :: v1.6.1 + Annotation Software version :: v1.5.0 Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.gff3 --- a/test-data/TEST_2/TEST_2.gff3 Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.gff3 Mon Jan 23 16:29:03 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: v1.6.1 +# Software: v1.5.0 # Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.hypotheticals.faa Mon Jan 23 16:29:03 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.hypotheticals.tsv --- a/test-data/TEST_2/TEST_2.hypotheticals.tsv Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.hypotheticals.tsv Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta v1.6.1, https://github.com/oschwengers/bakta +#Annotated with Bakta v1.5.0, 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 c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.json --- a/test-data/TEST_2/TEST_2.json Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.json Mon Jan 23 16:29:03 2023 +0000 @@ -79,11 +79,11 @@ } ], "run": { - "start": "2022-12-19 10:20:43", - "end": "2022-12-19 10:20:45" + "start": "2022-09-16 07:32:09", + "end": "2022-09-16 07:32:10" }, "version": { - "bakta": "1.6.1", + "bakta": "1.5.0", "db": "4.0" } } \ No newline at end of file diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.log --- a/test-data/TEST_2/TEST_2.log Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.log Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,3 @@ - parse genome sequences... imported: 1 filtered & revised: 1 @@ -77,18 +76,17 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/4/working +export annotation results to: /tmp/tmpmnqj1xog/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 0:01 [mm:ss]. +Annotation successfully finished in 0:00 [mm:ss]. diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.svg --- a/test-data/TEST_2/TEST_2.svg Mon Jan 23 14:05:58 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2400 +0,0 @@ - - - diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.tsv --- a/test-data/TEST_2/TEST_2.tsv Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.tsv Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta +#Annotated with Bakta (v1.5.0): 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 c75629db91ff -r 8c7499c6f32a test-data/TEST_2/TEST_2.txt --- a/test-data/TEST_2/TEST_2.txt Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_2/TEST_2.txt Mon Jan 23 16:29:03 2023 +0000 @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.6.1 +Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.embl --- a/test-data/TEST_3/TEST_3.embl Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_3/TEST_3.embl Mon Jan 23 16:29:03 2023 +0000 @@ -8,15 +8,15 @@ OC . XX CC Annotated with Bakta -CC Software: v1.6.1 +CC Software: v1.5.0 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 :: 12/19/2022, 10:21:03 +CC Annotation Date :: 09/16/2022, 07:32:21 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.6.1 +CC Annotation Software version :: v1.5.0 CC Annotation Database version :: v4.0 CC CDSs :: 0 CC tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.faa diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.fna Mon Jan 23 16:29:03 2023 +0000 @@ -0,0 +1,24 @@ +>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 c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.gbff --- a/test-data/TEST_3/TEST_3.gbff Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_3/TEST_3.gbff Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS contig_1 1330 bp DNA circular BCT 19-DEC-2022 +LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022 DEFINITION plasmid unnamed1, complete sequence. ACCESSION contig_1 VERSION contig_1 @@ -7,15 +7,15 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.6.1 + Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 12/19/2022, 10:21:03 + Annotation Date :: 09/16/2022, 07:32:21 Annotation Pipeline :: Bakta - Annotation Software version :: v1.6.1 + Annotation Software version :: v1.5.0 Annotation Database version :: v4.0 CDSs :: 0 tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.gff3 --- a/test-data/TEST_3/TEST_3.gff3 Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_3/TEST_3.gff3 Mon Jan 23 16:29:03 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: v1.6.1 +# Software: v1.5.0 # Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.json --- a/test-data/TEST_3/TEST_3.json Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_3/TEST_3.json Mon Jan 23 16:29:03 2023 +0000 @@ -32,11 +32,11 @@ } ], "run": { - "start": "2022-12-19 10:21:02", - "end": "2022-12-19 10:21:03" + "start": "2022-09-16 07:32:20", + "end": "2022-09-16 07:32:21" }, "version": { - "bakta": "1.6.1", + "bakta": "1.5.0", "db": "4.0" } } \ No newline at end of file diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.log --- a/test-data/TEST_3/TEST_3.log Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_3/TEST_3.log Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,3 @@ - parse genome sequences... imported: 1 filtered & revised: 1 @@ -43,14 +42,13 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/6/working +export annotation results to: /tmp/tmpmnqj1xog/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 c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.svg --- a/test-data/TEST_3/TEST_3.svg Mon Jan 23 14:05:58 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2397 +0,0 @@ - - - diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_3/TEST_3.tsv --- a/test-data/TEST_3/TEST_3.tsv Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_3/TEST_3.tsv Mon Jan 23 16:29:03 2023 +0000 @@ -1,3 +1,3 @@ -#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta +#Annotated with Bakta (v1.5.0): 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 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.embl --- a/test-data/TEST_4/TEST_4.embl Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.embl Mon Jan 23 16:29:03 2023 +0000 @@ -8,15 +8,15 @@ OC . XX CC Annotated with Bakta -CC Software: v1.6.1 +CC Software: v1.5.0 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 :: 12/19/2022, 10:21:31 +CC Annotation Date :: 09/16/2022, 07:32:50 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.6.1 +CC Annotation Software version :: v1.5.0 CC Annotation Database version :: v4.0 CC CDSs :: 2 CC tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.faa Mon Jan 23 16:29:03 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.fna Mon Jan 23 16:29:03 2023 +0000 @@ -0,0 +1,24 @@ +>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 c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.gbff --- a/test-data/TEST_4/TEST_4.gbff Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.gbff Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS p2 1330 bp DNA circular BCT 19-DEC-2022 +LOCUS p2 1330 bp DNA circular BCT 16-SEP-2022 DEFINITION plasmid pOSAK1, complete sequence. ACCESSION p2 VERSION p2 @@ -7,15 +7,15 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.6.1 + Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 12/19/2022, 10:21:31 + Annotation Date :: 09/16/2022, 07:32:50 Annotation Pipeline :: Bakta - Annotation Software version :: v1.6.1 + Annotation Software version :: v1.5.0 Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.gff3 --- a/test-data/TEST_4/TEST_4.gff3 Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.gff3 Mon Jan 23 16:29:03 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: v1.6.1 +# Software: v1.5.0 # Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.hypotheticals.faa Mon Jan 23 16:29:03 2023 +0000 @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.hypotheticals.tsv --- a/test-data/TEST_4/TEST_4.hypotheticals.tsv Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.hypotheticals.tsv Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta v1.6.1, https://github.com/oschwengers/bakta +#Annotated with Bakta v1.5.0, 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 c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.json --- a/test-data/TEST_4/TEST_4.json Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.json Mon Jan 23 16:29:03 2023 +0000 @@ -79,11 +79,11 @@ } ], "run": { - "start": "2022-12-19 10:21:29", - "end": "2022-12-19 10:21:31" + "start": "2022-09-16 07:32:48", + "end": "2022-09-16 07:32:50" }, "version": { - "bakta": "1.6.1", + "bakta": "1.5.0", "db": "4.0" } } \ No newline at end of file diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.log --- a/test-data/TEST_4/TEST_4.log Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.log Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,3 @@ - parse genome sequences... imported: 1 filtered & revised: 1 @@ -80,14 +79,13 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmptbkng6kx/job_working_directory/000/12/working +export annotation results to: /tmp/tmpmnqj1xog/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 c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.svg --- a/test-data/TEST_4/TEST_4.svg Mon Jan 23 14:05:58 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2400 +0,0 @@ - - - diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.tsv --- a/test-data/TEST_4/TEST_4.tsv Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.tsv Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,4 @@ -#Annotated with Bakta (v1.6.1): https://github.com/oschwengers/bakta +#Annotated with Bakta (v1.5.0): 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 c75629db91ff -r 8c7499c6f32a test-data/TEST_4/TEST_4.txt --- a/test-data/TEST_4/TEST_4.txt Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_4/TEST_4.txt Mon Jan 23 16:29:03 2023 +0000 @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.6.1 +Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/TEST_5/TEST_5.log --- a/test-data/TEST_5/TEST_5.log Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_5/TEST_5.log Mon Jan 23 16:29:03 2023 +0000 @@ -1,4 +1,3 @@ - parse genome sequences... imported: 1 filtered & revised: 1 @@ -43,14 +42,13 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/14/working +export annotation results to: /tmp/tmpmnqj1xog/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 c75629db91ff -r 8c7499c6f32a test-data/TEST_5/TEST_5.txt --- a/test-data/TEST_5/TEST_5.txt Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/TEST_5/TEST_5.txt Mon Jan 23 16:29:03 2023 +0000 @@ -24,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.6.1 +Software: v1.5.0 Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta diff -r c75629db91ff -r 8c7499c6f32a test-data/amrfinderplus_database.loc --- a/test-data/amrfinderplus_database.loc Mon Jan 23 14:05:58 2023 +0000 +++ b/test-data/amrfinderplus_database.loc Mon Jan 23 16:29:03 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/latest -amrfinderplus_V3.6_2020-03-20.1 V3.6-2020-03-20.1 ${__HERE__}/amrfinderplus-db/latest +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 diff -r c75629db91ff -r 8c7499c6f32a tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Mon Jan 23 14:05:58 2023 +0000 +++ b/tool_data_table_conf.xml.test Mon Jan 23 16:29:03 2023 +0000 @@ -7,6 +7,5 @@ value, name, path -