| Previous changeset 0:1a27ad3d0cdf (2022-09-01) Next changeset 2:debdc1469b41 (2022-12-21) |
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Commit message:
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 0ef6e6b2dcc9a41b32741368a60b931f31934686 |
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modified:
bakta.xml macro.xml test-data/TEST_1/TEST_1.embl test-data/TEST_1/TEST_1.gbff test-data/TEST_1/TEST_1.gff3 test-data/TEST_1/TEST_1.hypotheticals.tsv test-data/TEST_1/TEST_1.json test-data/TEST_1/TEST_1.log test-data/TEST_1/TEST_1.tsv test-data/TEST_1/TEST_1.txt test-data/TEST_2/TEST_2.embl test-data/TEST_2/TEST_2.gbff test-data/TEST_2/TEST_2.gff3 test-data/TEST_2/TEST_2.hypotheticals.tsv test-data/TEST_2/TEST_2.json test-data/TEST_2/TEST_2.log test-data/TEST_2/TEST_2.tsv test-data/TEST_2/TEST_2.txt test-data/TEST_3/TEST_3.embl test-data/TEST_3/TEST_3.gbff test-data/TEST_3/TEST_3.gff3 test-data/TEST_3/TEST_3.json test-data/TEST_3/TEST_3.log test-data/TEST_3/TEST_3.tsv test-data/TEST_4/TEST_4.embl test-data/TEST_4/TEST_4.gbff test-data/TEST_4/TEST_4.gff3 test-data/TEST_4/TEST_4.hypotheticals.tsv test-data/TEST_4/TEST_4.json test-data/TEST_4/TEST_4.log test-data/TEST_4/TEST_4.tsv test-data/TEST_4/TEST_4.txt test-data/TEST_5/TEST_5.log test-data/TEST_5/TEST_5.txt test-data/test-db/bakta.db test-data/test-db/version.json |
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removed:
test-data/tmp/NC_002127.1.fna test-data/tmp/TEST_1/TEST_1.embl test-data/tmp/TEST_1/TEST_1.faa test-data/tmp/TEST_1/TEST_1.ffn test-data/tmp/TEST_1/TEST_1.fna test-data/tmp/TEST_1/TEST_1.gbff test-data/tmp/TEST_1/TEST_1.gff3 test-data/tmp/TEST_1/TEST_1.hypotheticals.faa test-data/tmp/TEST_1/TEST_1.hypotheticals.tsv test-data/tmp/TEST_1/TEST_1.json test-data/tmp/TEST_1/TEST_1.log test-data/tmp/TEST_1/TEST_1.tsv test-data/tmp/TEST_1/TEST_1.txt test-data/tmp/TEST_2/TEST_2.embl test-data/tmp/TEST_2/TEST_2.faa test-data/tmp/TEST_2/TEST_2.ffn test-data/tmp/TEST_2/TEST_2.fna test-data/tmp/TEST_2/TEST_2.gbff test-data/tmp/TEST_2/TEST_2.gff3 test-data/tmp/TEST_2/TEST_2.hypotheticals.faa test-data/tmp/TEST_2/TEST_2.hypotheticals.tsv test-data/tmp/TEST_2/TEST_2.json test-data/tmp/TEST_2/TEST_2.log test-data/tmp/TEST_2/TEST_2.tsv test-data/tmp/TEST_2/TEST_2.txt test-data/tmp/TEST_3/TEST_3.embl test-data/tmp/TEST_3/TEST_3.faa test-data/tmp/TEST_3/TEST_3.ffn test-data/tmp/TEST_3/TEST_3.fna test-data/tmp/TEST_3/TEST_3.gbff test-data/tmp/TEST_3/TEST_3.gff3 test-data/tmp/TEST_3/TEST_3.json test-data/tmp/TEST_3/TEST_3.log test-data/tmp/TEST_3/TEST_3.tsv test-data/tmp/TEST_3/TEST_3.txt test-data/tmp/TEST_4/TEST_4.embl test-data/tmp/TEST_4/TEST_4.faa test-data/tmp/TEST_4/TEST_4.ffn test-data/tmp/TEST_4/TEST_4.fna test-data/tmp/TEST_4/TEST_4.gbff test-data/tmp/TEST_4/TEST_4.gff3 test-data/tmp/TEST_4/TEST_4.hypotheticals.faa test-data/tmp/TEST_4/TEST_4.hypotheticals.tsv test-data/tmp/TEST_4/TEST_4.json test-data/tmp/TEST_4/TEST_4.log test-data/tmp/TEST_4/TEST_4.tsv test-data/tmp/TEST_4/TEST_4.txt test-data/tmp/TEST_5/TEST_5.log test-data/tmp/TEST_5/TEST_5.txt test-data/tmp/prodigal.tf test-data/tmp/replicons.tsv test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pdb test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.phr test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pin test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.psq test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.ptf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pto test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.not test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/fam.tab test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/version.txt test-data/tmp/test-db/antifam.h3f test-data/tmp/test-db/antifam.h3i test-data/tmp/test-db/antifam.h3m test-data/tmp/test-db/antifam.h3p test-data/tmp/test-db/bakta.db test-data/tmp/test-db/expert-protein-sequences.dmnd test-data/tmp/test-db/ncRNA-genes.i1f test-data/tmp/test-db/ncRNA-genes.i1i test-data/tmp/test-db/ncRNA-genes.i1m test-data/tmp/test-db/ncRNA-genes.i1p test-data/tmp/test-db/ncRNA-regions.i1f test-data/tmp/test-db/ncRNA-regions.i1i test-data/tmp/test-db/ncRNA-regions.i1m test-data/tmp/test-db/ncRNA-regions.i1p test-data/tmp/test-db/oric.fna test-data/tmp/test-db/orit.fna test-data/tmp/test-db/pfam.h3f test-data/tmp/test-db/pfam.h3i test-data/tmp/test-db/pfam.h3m test-data/tmp/test-db/pfam.h3p test-data/tmp/test-db/psc.dmnd test-data/tmp/test-db/rRNA.i1f test-data/tmp/test-db/rRNA.i1i test-data/tmp/test-db/rRNA.i1m test-data/tmp/test-db/rRNA.i1p test-data/tmp/test-db/rfam-go.tsv test-data/tmp/test-db/sorf.dmnd test-data/tmp/test-db/version.json test-data/tmp/test_database.loc test-data/tmp/user-proteins.faa |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e bakta.xml --- a/bakta.xml Thu Sep 01 17:28:43 2022 +0000 +++ b/bakta.xml Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -233,10 +233,10 @@ <param name="db_select" value="test-db-bakta"/> <param name="input_file" value="NC_002127.1.fna"/> </section> - <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="4"> + <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="10"> <assert_contents> <has_text_matching n="1" expression="Genome size: 1,330 bp"/> - <has_n_lines n="90" delta="1"/> + <has_n_lines n="94" delta="1"/> </assert_contents> </output> <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="1"/> |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e macro.xml --- a/macro.xml Thu Sep 01 17:28:43 2022 +0000 +++ b/macro.xml Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.4.2</token> + <token name="@TOOL_VERSION@">1.5.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.embl --- a/test-data/TEST_1/TEST_1.embl Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.embl Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -8,16 +8,16 @@ OC . XX CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 +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 :: 08/22/2022, 13:06:54 +CC Annotation Date :: 09/16/2022, 07:31:59 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 +CC Annotation Software version :: v1.5.0 +CC Annotation Database version :: v4.0 CC CDSs :: 2 CC tRNAs :: 0 CC tmRNAs :: 0 @@ -28,6 +28,7 @@ CC oriCs/oriVs :: 0 CC oriTs :: 0 CC gaps :: 0 +CC pseudogenes :: 0 XX FH Key Location/Qualifiers FH @@ -39,25 +40,25 @@ FT CDS 413..736 FT /product="hypothetical protein" FT /locus_tag="IHHALP_00005" +FT /protein_id="gnl|Bakta|IHHALP_00005" FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL FT MAD" FT /codon_start=1 FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00005" FT /inference="ab initio prediction:Prodigal:2.6" FT gene complement(join(971..1330,1..141)) FT /locus_tag="IHHALP_00010" FT CDS complement(join(971..1330,1..141)) FT /product="hypothetical protein" FT /locus_tag="IHHALP_00010" +FT /protein_id="gnl|Bakta|IHHALP_00010" FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG FT IPI" FT /codon_start=1 FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00010" FT /inference="ab initio prediction:Prodigal:2.6" XX SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.gbff --- a/test-data/TEST_1/TEST_1.gbff Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.gbff Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -1,4 +1,4 @@ -LOCUS contig_1 1330 bp DNA circular BCT 22-AUG-2022 +LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022 DEFINITION plasmid unnamed1, complete sequence. ACCESSION contig_1 VERSION contig_1 @@ -7,16 +7,16 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 + Software: v1.5.0 + Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 13:06:54 + Annotation Date :: 09/16/2022, 07:31:59 Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 + Annotation Software version :: v1.5.0 + Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 tmRNAs :: 0 @@ -27,6 +27,7 @@ oriCs/oriVs :: 0 oriTs :: 0 gaps :: 0 + pseudogenes :: 0 FEATURES Location/Qualifiers source 1..1330 /mol_type="genomic DNA" @@ -36,25 +37,25 @@ CDS 413..736 /product="hypothetical protein" /locus_tag="IHHALP_00005" + /protein_id="gnl|Bakta|IHHALP_00005" /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL MAD" /codon_start=1 /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00005" /inference="ab initio prediction:Prodigal:2.6" gene complement(join(971..1330,1..141)) /locus_tag="IHHALP_00010" CDS complement(join(971..1330,1..141)) /product="hypothetical protein" /locus_tag="IHHALP_00010" + /protein_id="gnl|Bakta|IHHALP_00010" /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG IPI" /codon_start=1 /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00010" /inference="ab initio prediction:Prodigal:2.6" ORIGIN 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.gff3 --- a/test-data/TEST_1/TEST_1.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.gff3 Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -1,8 +1,8 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.4.2 -# Database: v3.0 +# Software: v1.5.0 +# Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region contig_1 1 1330 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.hypotheticals.tsv --- a/test-data/TEST_1/TEST_1.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv Fri Sep 16 13:42:15 2022 +0000 |
| [ |
| @@ -1,5 +1,5 @@ -#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta -#Database v3.0, https://doi.org/10.5281/zenodo.4247252 +#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 contig_1 971 141 - IHHALP_00010 18.9 7.7 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.json --- a/test-data/TEST_1/TEST_1.json Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.json Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -80,11 +80,11 @@ } ], "run": { - "start": "2022-08-22 13:06:53", - "end": "2022-08-22 13:06:54" + "start": "2022-09-16 07:31:58", + "end": "2022-09-16 07:31:59" }, "version": { - "bakta": "1.4.2", - "db": "3.0" + "bakta": "1.5.0", + "db": "4.0" } } \ No newline at end of file |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.log --- a/test-data/TEST_1/TEST_1.log Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.log Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -28,7 +28,10 @@ amrfinder: 0 protein sequences: 0 combine annotations and mark hypotheticals... - analyze hypothetical proteins: 2 + detect pseudogenes... + pseudogene candidates: 0 + found pseudogenes: 0 +analyze hypothetical proteins: 2 detected Pfam hits: 0 calculated proteins statistics revise special cases... @@ -68,13 +71,14 @@ CRISPR arrays: 0 CDSs: 2 hypotheticals: 2 + pseudogenes: 0 signal peptides: 0 sORFs: 0 gaps: 0 oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpb092rhfs/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... |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.tsv --- a/test-data/TEST_1/TEST_1.tsv Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.tsv Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -1,5 +1,5 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): https://doi.org/10.5281/zenodo.4247252 +#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 contig_1 cds 971 141 - IHHALP_00010 hypothetical protein |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_1/TEST_1.txt --- a/test-data/TEST_1/TEST_1.txt Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_1/TEST_1.txt Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -14,6 +14,7 @@ ncRNA regions: 0 CRISPR arrays: 0 CDSs: 2 +pseudogenes: 0 hypotheticals: 2 signal peptides: 0 sORFs: 0 @@ -23,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.4.2 -Database: v3.0 +Software: v1.5.0 +Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.embl --- a/test-data/TEST_2/TEST_2.embl Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.embl Fri Sep 16 13:42:15 2022 +0000 |
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| @@ -8,16 +8,16 @@ OC . XX CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 +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 :: 08/22/2022, 13:07:08 +CC Annotation Date :: 09/16/2022, 07:32:10 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 +CC Annotation Software version :: v1.5.0 +CC Annotation Database version :: v4.0 CC CDSs :: 2 CC tRNAs :: 0 CC tmRNAs :: 0 @@ -28,6 +28,7 @@ CC oriCs/oriVs :: 0 CC oriTs :: 0 CC gaps :: 0 +CC pseudogenes :: 0 XX FH Key Location/Qualifiers FH @@ -41,25 +42,25 @@ FT CDS 413..736 FT /product="hypothetical protein" FT /locus_tag="IHHALP_00005" +FT /protein_id="gnl|Bakta|IHHALP_00005" FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL FT MAD" FT /codon_start=1 FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00005" FT /inference="ab initio prediction:Prodigal:2.6" FT gene complement(join(971..1330,1..141)) FT /locus_tag="IHHALP_00010" FT CDS complement(join(971..1330,1..141)) FT /product="hypothetical protein" FT /locus_tag="IHHALP_00010" +FT /protein_id="gnl|Bakta|IHHALP_00010" FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG FT IPI" FT /codon_start=1 FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00010" FT /inference="ab initio prediction:Prodigal:2.6" XX SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.gbff --- a/test-data/TEST_2/TEST_2.gbff Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.gbff Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -LOCUS NC_002127.1 1330 bp DNA circular BCT 22-AUG-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 @@ -7,16 +7,16 @@ ORGANISM Escherichia coli o157:h7 Sakai . COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 + Software: v1.5.0 + Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 13:07:08 + Annotation Date :: 09/16/2022, 07:32:10 Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 + Annotation Software version :: v1.5.0 + Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 tmRNAs :: 0 @@ -27,6 +27,7 @@ oriCs/oriVs :: 0 oriTs :: 0 gaps :: 0 + pseudogenes :: 0 FEATURES Location/Qualifiers source 1..1330 /mol_type="genomic DNA" @@ -38,25 +39,25 @@ CDS 413..736 /product="hypothetical protein" /locus_tag="IHHALP_00005" + /protein_id="gnl|Bakta|IHHALP_00005" /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL MAD" /codon_start=1 /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00005" /inference="ab initio prediction:Prodigal:2.6" gene complement(join(971..1330,1..141)) /locus_tag="IHHALP_00010" CDS complement(join(971..1330,1..141)) /product="hypothetical protein" /locus_tag="IHHALP_00010" + /protein_id="gnl|Bakta|IHHALP_00010" /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG IPI" /codon_start=1 /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00010" /inference="ab initio prediction:Prodigal:2.6" ORIGIN 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.gff3 --- a/test-data/TEST_2/TEST_2.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.gff3 Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -2,8 +2,8 @@ ##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: v1.4.2 -# Database: v3.0 +# Software: v1.5.0 +# Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region NC_002127.1 1 1330 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.hypotheticals.tsv --- a/test-data/TEST_2/TEST_2.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.hypotheticals.tsv Fri Sep 16 13:42:15 2022 +0000 |
| [ |
| @@ -1,5 +1,5 @@ -#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta -#Database v3.0, https://doi.org/10.5281/zenodo.4247252 +#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 NC_002127.1 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.json --- a/test-data/TEST_2/TEST_2.json Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.json Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -79,11 +79,11 @@ } ], "run": { - "start": "2022-08-22 13:07:07", - "end": "2022-08-22 13:07:08" + "start": "2022-09-16 07:32:09", + "end": "2022-09-16 07:32:10" }, "version": { - "bakta": "1.4.2", - "db": "3.0" + "bakta": "1.5.0", + "db": "4.0" } } \ No newline at end of file |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.log --- a/test-data/TEST_2/TEST_2.log Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.log Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -26,7 +26,10 @@ amrfinder: 0 protein sequences: 0 combine annotations and mark hypotheticals... - analyze hypothetical proteins: 2 + detect pseudogenes... + pseudogene candidates: 0 + found pseudogenes: 0 +analyze hypothetical proteins: 2 detected Pfam hits: 0 calculated proteins statistics revise special cases... @@ -66,13 +69,14 @@ CRISPR arrays: 0 CDSs: 2 hypotheticals: 2 + pseudogenes: 0 signal peptides: 0 sORFs: 0 gaps: 0 oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpb092rhfs/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... |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.tsv --- a/test-data/TEST_2/TEST_2.tsv Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.tsv Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,5 +1,5 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): https://doi.org/10.5281/zenodo.4247252 +#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 NC_002127.1 cds 971 141 - IHHALP_00010 hypothetical protein |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_2/TEST_2.txt --- a/test-data/TEST_2/TEST_2.txt Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_2/TEST_2.txt Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -14,6 +14,7 @@ ncRNA regions: 0 CRISPR arrays: 0 CDSs: 2 +pseudogenes: 0 hypotheticals: 2 signal peptides: 0 sORFs: 0 @@ -23,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.4.2 -Database: v3.0 +Software: v1.5.0 +Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_3/TEST_3.embl --- a/test-data/TEST_3/TEST_3.embl Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_3/TEST_3.embl Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -8,16 +8,16 @@ OC . XX CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 +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 :: 08/22/2022, 13:07:22 +CC Annotation Date :: 09/16/2022, 07:32:21 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 +CC Annotation Software version :: v1.5.0 +CC Annotation Database version :: v4.0 CC CDSs :: 0 CC tRNAs :: 0 CC tmRNAs :: 0 @@ -28,6 +28,7 @@ CC oriCs/oriVs :: 0 CC oriTs :: 0 CC gaps :: 0 +CC pseudogenes :: 0 XX FH Key Location/Qualifiers FH |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_3/TEST_3.gbff --- a/test-data/TEST_3/TEST_3.gbff Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_3/TEST_3.gbff Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -LOCUS contig_1 1330 bp DNA circular BCT 22-AUG-2022 +LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022 DEFINITION plasmid unnamed1, complete sequence. ACCESSION contig_1 VERSION contig_1 @@ -7,16 +7,16 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 + Software: v1.5.0 + Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 13:07:22 + Annotation Date :: 09/16/2022, 07:32:21 Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 + Annotation Software version :: v1.5.0 + Annotation Database version :: v4.0 CDSs :: 0 tRNAs :: 0 tmRNAs :: 0 @@ -27,6 +27,7 @@ oriCs/oriVs :: 0 oriTs :: 0 gaps :: 0 + pseudogenes :: 0 FEATURES Location/Qualifiers source 1..1330 /mol_type="genomic DNA" |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_3/TEST_3.gff3 --- a/test-data/TEST_3/TEST_3.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_3/TEST_3.gff3 Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,8 +1,8 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.4.2 -# Database: v3.0 +# Software: v1.5.0 +# Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region contig_1 1 1330 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_3/TEST_3.json --- a/test-data/TEST_3/TEST_3.json Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_3/TEST_3.json Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -32,11 +32,11 @@ } ], "run": { - "start": "2022-08-22 13:07:21", - "end": "2022-08-22 13:07:22" + "start": "2022-09-16 07:32:20", + "end": "2022-09-16 07:32:21" }, "version": { - "bakta": "1.4.2", - "db": "3.0" + "bakta": "1.5.0", + "db": "4.0" } } \ No newline at end of file |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_3/TEST_3.log --- a/test-data/TEST_3/TEST_3.log Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_3/TEST_3.log Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -35,13 +35,14 @@ CRISPR arrays: 0 CDSs: 0 hypotheticals: 0 + pseudogenes: 0 signal peptides: 0 sORFs: 0 gaps: 0 oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpb092rhfs/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... |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_3/TEST_3.tsv --- a/test-data/TEST_3/TEST_3.tsv Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_3/TEST_3.tsv Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,3 +1,3 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): https://doi.org/10.5281/zenodo.4247252 +#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 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.embl --- a/test-data/TEST_4/TEST_4.embl Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.embl Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -8,16 +8,16 @@ OC . XX CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 +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 :: 08/22/2022, 13:08:00 +CC Annotation Date :: 09/16/2022, 07:32:50 CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 +CC Annotation Software version :: v1.5.0 +CC Annotation Database version :: v4.0 CC CDSs :: 2 CC tRNAs :: 0 CC tmRNAs :: 0 @@ -28,6 +28,7 @@ CC oriCs/oriVs :: 0 CC oriTs :: 0 CC gaps :: 0 +CC pseudogenes :: 0 XX FH Key Location/Qualifiers FH @@ -39,25 +40,25 @@ FT CDS 413..736 FT /product="hypothetical protein" FT /locus_tag="IHHALP_00005" +FT /protein_id="gnl|Bakta|IHHALP_00005" FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL FT MAD" FT /codon_start=1 FT /transl_table=4 -FT /protein_id="gnl|Bakta|IHHALP_00005" FT /inference="ab initio prediction:Prodigal:2.6" FT gene complement(join(971..1330,1..141)) FT /locus_tag="IHHALP_00010" FT CDS complement(join(971..1330,1..141)) FT /product="hypothetical protein" FT /locus_tag="IHHALP_00010" +FT /protein_id="gnl|Bakta|IHHALP_00010" FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG FT IPI" FT /codon_start=1 FT /transl_table=4 -FT /protein_id="gnl|Bakta|IHHALP_00010" FT /inference="ab initio prediction:Prodigal:2.6" XX SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.gbff --- a/test-data/TEST_4/TEST_4.gbff Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.gbff Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -LOCUS p2 1330 bp DNA circular BCT 22-AUG-2022 +LOCUS p2 1330 bp DNA circular BCT 16-SEP-2022 DEFINITION plasmid pOSAK1, complete sequence. ACCESSION p2 VERSION p2 @@ -7,16 +7,16 @@ ORGANISM . . COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 + Software: v1.5.0 + Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 13:08:00 + Annotation Date :: 09/16/2022, 07:32:50 Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 + Annotation Software version :: v1.5.0 + Annotation Database version :: v4.0 CDSs :: 2 tRNAs :: 0 tmRNAs :: 0 @@ -27,6 +27,7 @@ oriCs/oriVs :: 0 oriTs :: 0 gaps :: 0 + pseudogenes :: 0 FEATURES Location/Qualifiers source 1..1330 /mol_type="genomic DNA" @@ -36,25 +37,25 @@ CDS 413..736 /product="hypothetical protein" /locus_tag="IHHALP_00005" + /protein_id="gnl|Bakta|IHHALP_00005" /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL MAD" /codon_start=1 /transl_table=4 - /protein_id="gnl|Bakta|IHHALP_00005" /inference="ab initio prediction:Prodigal:2.6" gene complement(join(971..1330,1..141)) /locus_tag="IHHALP_00010" CDS complement(join(971..1330,1..141)) /product="hypothetical protein" /locus_tag="IHHALP_00010" + /protein_id="gnl|Bakta|IHHALP_00010" /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG IPI" /codon_start=1 /transl_table=4 - /protein_id="gnl|Bakta|IHHALP_00010" /inference="ab initio prediction:Prodigal:2.6" ORIGIN 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.gff3 --- a/test-data/TEST_4/TEST_4.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.gff3 Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,8 +1,8 @@ ##gff-version 3 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo # Annotated with Bakta -# Software: v1.4.2 -# Database: v3.0 +# Software: v1.5.0 +# Database: v4.0 # DOI: 10.1099/mgen.0.000685 # URL: github.com/oschwengers/bakta ##sequence-region p2 1 1330 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.hypotheticals.tsv --- a/test-data/TEST_4/TEST_4.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.hypotheticals.tsv Fri Sep 16 13:42:15 2022 +0000 |
| [ |
| @@ -1,5 +1,5 @@ -#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta -#Database v3.0, https://doi.org/10.5281/zenodo.4247252 +#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 p2 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.json --- a/test-data/TEST_4/TEST_4.json Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.json Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -79,11 +79,11 @@ } ], "run": { - "start": "2022-08-22 13:07:59", - "end": "2022-08-22 13:08:00" + "start": "2022-09-16 07:32:48", + "end": "2022-09-16 07:32:50" }, "version": { - "bakta": "1.4.2", - "db": "3.0" + "bakta": "1.5.0", + "db": "4.0" } } \ No newline at end of file |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.log --- a/test-data/TEST_4/TEST_4.log Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.log Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -29,7 +29,10 @@ protein sequences: 0 user protein sequences: 0 combine annotations and mark hypotheticals... - analyze hypothetical proteins: 2 + detect pseudogenes... + pseudogene candidates: 0 + found pseudogenes: 0 +analyze hypothetical proteins: 2 detected Pfam hits: 0 calculated proteins statistics revise special cases... @@ -69,13 +72,14 @@ CRISPR arrays: 0 CDSs: 2 hypotheticals: 2 + pseudogenes: 0 signal peptides: 0 sORFs: 0 gaps: 0 oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpb092rhfs/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... |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.tsv --- a/test-data/TEST_4/TEST_4.tsv Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.tsv Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -1,5 +1,5 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): https://doi.org/10.5281/zenodo.4247252 +#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 p2 cds 971 141 - IHHALP_00010 hypothetical protein |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_4/TEST_4.txt --- a/test-data/TEST_4/TEST_4.txt Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_4/TEST_4.txt Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -14,6 +14,7 @@ ncRNA regions: 0 CRISPR arrays: 0 CDSs: 2 +pseudogenes: 0 hypotheticals: 2 signal peptides: 0 sORFs: 0 @@ -23,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.4.2 -Database: v3.0 +Software: v1.5.0 +Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_5/TEST_5.log --- a/test-data/TEST_5/TEST_5.log Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_5/TEST_5.log Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -35,13 +35,14 @@ CRISPR arrays: 0 CDSs: 0 hypotheticals: 0 + pseudogenes: 0 signal peptides: 0 sORFs: 0 gaps: 0 oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpb092rhfs/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... |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/TEST_5/TEST_5.txt --- a/test-data/TEST_5/TEST_5.txt Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/TEST_5/TEST_5.txt Fri Sep 16 13:42:15 2022 +0000 |
| b |
| @@ -14,6 +14,7 @@ ncRNA regions: 0 CRISPR arrays: 0 CDSs: 0 +pseudogenes: 0 hypotheticals: 0 signal peptides: 0 sORFs: 0 @@ -23,7 +24,7 @@ oriTs: 0 Bakta: -Software: v1.4.2 -Database: v3.0 +Software: v1.5.0 +Database: v4.0 DOI: 10.1099/mgen.0.000685 URL: github.com/oschwengers/bakta |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/test-db/bakta.db |
| b |
| Binary file test-data/test-db/bakta.db has changed |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/test-db/version.json --- a/test-data/test-db/version.json Thu Sep 01 17:28:43 2022 +0000 +++ b/test-data/test-db/version.json Fri Sep 16 13:42:15 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ { - "date": "2021-08-9", - "major": 3, + "date": "2022-08-25", + "major": 4, "minor": 0, "dependencies": [ { |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/NC_002127.1.fna --- a/test-data/tmp/NC_002127.1.fna Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ ->NC_002127.1 Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTT -TCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCA -TCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGT -CTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGC -TTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTA -TTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAG -GAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTA -AGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAA -ACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTAT -CACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTA -TGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGT -TCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGA -ATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTT -TAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTA -ACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATT -AAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.embl --- a/test-data/tmp/TEST_1/TEST_1.embl Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,87 +0,0 @@ -ID contig_1; ; circular; DNA; ; PRO; 1330 BP. -XX -AC contig_1; -XX -DE plasmid unnamed1, complete sequence -XX -OS . -OC . -XX -CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 08/22/2022, 12:57:48 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 -CC CDSs :: 2 -CC tRNAs :: 0 -CC tmRNAs :: 0 -CC rRNAs :: 0 -CC ncRNAs :: 0 -CC regulatory ncRNAs :: 0 -CC CRISPR Arrays :: 0 -CC oriCs/oriVs :: 0 -CC oriTs :: 0 -CC gaps :: 0 -XX -FH Key Location/Qualifiers -FH -FT source 1..1330 -FT /mol_type="genomic DNA" -FT /plasmid="unnamed1" -FT gene 413..736 -FT /locus_tag="IHHALP_00005" -FT CDS 413..736 -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00005" -FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA -FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL -FT MAD" -FT /codon_start=1 -FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00005" -FT /inference="ab initio prediction:Prodigal:2.6" -FT gene complement(join(971..1330,1..141)) -FT /locus_tag="IHHALP_00010" -FT CDS complement(join(971..1330,1..141)) -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00010" -FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA -FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR -FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG -FT IPI" -FT /codon_start=1 -FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00010" -FT /inference="ab initio prediction:Prodigal:2.6" -XX -SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; - ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 - gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 - agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 - tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 - tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 - gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 - cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 - acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 - agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 - acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 - agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 - cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 - gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 - aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 - tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 - agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 - tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 - ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 - cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 - taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 - aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 - tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 - cttctatttg 1330 -// |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.faa --- a/test-data/tmp/TEST_1/TEST_1.faa Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.ffn --- a/test-data/tmp/TEST_1/TEST_1.ffn Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.fna --- a/test-data/tmp/TEST_1/TEST_1.fna Thu Sep 01 17:28:43 2022 +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 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.gbff --- a/test-data/tmp/TEST_1/TEST_1.gbff Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,83 +0,0 @@ -LOCUS contig_1 1330 bp DNA circular BCT 22-AUG-2022 -DEFINITION plasmid unnamed1, complete sequence. -ACCESSION contig_1 -VERSION contig_1 -KEYWORDS . -SOURCE None - ORGANISM . - . -COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 12:57:48 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 - CDSs :: 2 - tRNAs :: 0 - tmRNAs :: 0 - rRNAs :: 0 - ncRNAs :: 0 - regulatory ncRNAs :: 0 - CRISPR Arrays :: 0 - oriCs/oriVs :: 0 - oriTs :: 0 - gaps :: 0 -FEATURES Location/Qualifiers - source 1..1330 - /mol_type="genomic DNA" - /plasmid="unnamed1" - gene 413..736 - /locus_tag="IHHALP_00005" - CDS 413..736 - /product="hypothetical protein" - /locus_tag="IHHALP_00005" - /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA - AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL - MAD" - /codon_start=1 - /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00005" - /inference="ab initio prediction:Prodigal:2.6" - gene complement(join(971..1330,1..141)) - /locus_tag="IHHALP_00010" - CDS complement(join(971..1330,1..141)) - /product="hypothetical protein" - /locus_tag="IHHALP_00010" - /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA - EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR - YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG - IPI" - /codon_start=1 - /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00010" - /inference="ab initio prediction:Prodigal:2.6" -ORIGIN - 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc - 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc - 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg - 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt - 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt - 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac - 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa - 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga - 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt - 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga - 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga - 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag - 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt - 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga - 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc - 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc - 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa - 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat - 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat - 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa - 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc - 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg - 1321 cttctatttg -// |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.gff3 --- a/test-data/tmp/TEST_1/TEST_1.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,36 +0,0 @@ -##gff-version 3 -##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo -# Annotated with Bakta -# Software: v1.4.2 -# Database: v3.0 -# DOI: 10.1099/mgen.0.000685 -# URL: github.com/oschwengers/bakta -##sequence-region contig_1 1 1330 -contig_1 Bakta region 1 1330 . + . ID=contig_1;Name=contig_1;Is_circular=true -contig_1 Prodigal CDS 413 736 . + 0 ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein -contig_1 Prodigal CDS 971 1471 . - 0 ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein -##FASTA ->contig_1 -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.hypotheticals.faa --- a/test-data/tmp/TEST_1/TEST_1.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.hypotheticals.tsv --- a/test-data/tmp/TEST_1/TEST_1.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta -#Database v3.0, 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 -contig_1 971 141 - IHHALP_00010 18.9 7.7 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.json --- a/test-data/tmp/TEST_1/TEST_1.json Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,90 +0,0 @@ -{ - "genome": { - "genus": null, - "species": null, - "strain": null, - "complete": true, - "gram": "?", - "translation_table": 11 - }, - "stats": { - "no_sequences": 1, - "size": 1330, - "gc": 0.4518796992481203, - "n_ratio": 0.0, - "n50": 1330, - "coding_ratio": 0.6203007518796992 - }, - "features": [ - { - "type": "cds", - "contig": "contig_1", - "start": 413, - "stop": 736, - "strand": "+", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "GGAG/GAGG", - "db_xrefs": [], - "frame": 2, - "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", - "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", - "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 12072.90819999999, - "isoelectric_point": 10.367886161804197 - }, - "id": "IHHALPPJCH_1", - "locus": "IHHALP_00005" - }, - { - "type": "cds", - "contig": "contig_1", - "start": 971, - "stop": 141, - "strand": "-", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "AGGA/GGAG/GAGG", - "db_xrefs": [], - "frame": 1, - "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", - "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", - "edge": true, - "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 18866.325799999995, - "isoelectric_point": 7.696590614318848 - }, - "id": "IHHALPPJCH_2", - "locus": "IHHALP_00010" - } - ], - "sequences": [ - { - "id": "contig_1", - "description": "[completeness=complete] [topology=circular] [gcode=11]", - "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", - "length": 1330, - "complete": true, - "type": "plasmid", - "topology": "circular", - "simple_id": "contig_1", - "orig_id": "NC_002127.1", - "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", - "name": "unnamed1" - } - ], - "run": { - "start": "2022-08-22 12:57:47", - "end": "2022-08-22 12:57:48" - }, - "version": { - "bakta": "1.4.2", - "db": "3.0" - } -} \ No newline at end of file |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.log --- a/test-data/tmp/TEST_1/TEST_1.log Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,90 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - plasmids: 1 - -start annotation... -predict tRNAs... - found: 0 -predict tmRNAs... - found: 0 -predict rRNAs... - found: 0 -predict ncRNAs... - found: 0 -predict ncRNA regions... - found: 0 -predict CRISPR arrays... - found: 0 -predict & annotate CDSs... - predicted: 2 - discarded spurious: 0 - revised translational exceptions: 0 - detected IPSs: 0 - found PSCs: 0 - found PSCCs: 0 - lookup annotations... - conduct expert systems... - amrfinder: 0 - protein sequences: 0 - combine annotations and mark hypotheticals... - analyze hypothetical proteins: 2 - detected Pfam hits: 0 - calculated proteins statistics - revise special cases... -extract sORF... - potential: 22 - discarded due to overlaps: 2 - discarded spurious: 0 - detected IPSs: 0 - found PSCs: 0 - lookup annotations... - filter and combine annotations... - filtered sORFs: 0 -detect gaps... - found: 0 -detect oriCs/oriVs... - found: 0 -detect oriTs... - found: 0 -apply feature overlap filters... -select features and create locus tags... -selected: 2 - -genome statistics: - Genome size: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - N ratio: 0.0 % - coding density: 62.0 % - -annotation summary: - tRNAs: 0 - tmRNAs: 0 - rRNAs: 0 - ncRNAs: 0 - ncRNA regions: 0 - CRISPR arrays: 0 - CDSs: 2 - hypotheticals: 2 - signal peptides: 0 - sORFs: 0 - gaps: 0 - oriCs/oriVs: 0 - oriTs: 0 - -export annotation results to: /tmp/tmpqcic3cc5/job_working_directory/000/2/working - human readable TSV... - GFF3... - INSDC GenBank & EMBL... - genome sequences... - feature nucleotide sequences... - translated CDS sequences... - 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]. |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.tsv --- a/test-data/tmp/TEST_1/TEST_1.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): 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 -contig_1 cds 971 141 - IHHALP_00010 hypothetical protein |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_1/TEST_1.txt --- a/test-data/tmp/TEST_1/TEST_1.txt Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,29 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 62.0 - -Annotation: -tRNAs: 0 -tmRNAs: 0 -rRNAs: 0 -ncRNAs: 0 -ncRNA regions: 0 -CRISPR arrays: 0 -CDSs: 2 -hypotheticals: 2 -signal peptides: 0 -sORFs: 0 -gaps: 0 -oriCs: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.4.2 -Database: v3.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.embl --- a/test-data/tmp/TEST_2/TEST_2.embl Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,89 +0,0 @@ -ID NC_002127; SV 1; circular; DNA; ; PRO; 1330 BP. -XX -AC NC_002127; -XX -DE Escherichia coli o157:h7 Sakai plasmid pOSAK1, complete sequence -XX -OS Escherichia coli o157:h7 Sakai -OC . -XX -CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 08/22/2022, 12:58:03 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 -CC CDSs :: 2 -CC tRNAs :: 0 -CC tmRNAs :: 0 -CC rRNAs :: 0 -CC ncRNAs :: 0 -CC regulatory ncRNAs :: 0 -CC CRISPR Arrays :: 0 -CC oriCs/oriVs :: 0 -CC oriTs :: 0 -CC gaps :: 0 -XX -FH Key Location/Qualifiers -FH -FT source 1..1330 -FT /mol_type="genomic DNA" -FT /organism="Escherichia coli o157:h7 Sakai" -FT /strain="Sakai" -FT /plasmid="pOSAK1" -FT gene 413..736 -FT /locus_tag="IHHALP_00005" -FT CDS 413..736 -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00005" -FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA -FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL -FT MAD" -FT /codon_start=1 -FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00005" -FT /inference="ab initio prediction:Prodigal:2.6" -FT gene complement(join(971..1330,1..141)) -FT /locus_tag="IHHALP_00010" -FT CDS complement(join(971..1330,1..141)) -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00010" -FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA -FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR -FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG -FT IPI" -FT /codon_start=1 -FT /transl_table=11 -FT /protein_id="gnl|Bakta|IHHALP_00010" -FT /inference="ab initio prediction:Prodigal:2.6" -XX -SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; - ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 - gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 - agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 - tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 - tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 - gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 - cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 - acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 - agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 - acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 - agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 - cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 - gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 - aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 - tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 - agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 - tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 - ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 - cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 - taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 - aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 - tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 - cttctatttg 1330 -// |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.faa --- a/test-data/tmp/TEST_2/TEST_2.faa Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.ffn --- a/test-data/tmp/TEST_2/TEST_2.ffn Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.fna --- a/test-data/tmp/TEST_2/TEST_2.fna Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.gbff --- a/test-data/tmp/TEST_2/TEST_2.gbff Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,85 +0,0 @@ -LOCUS NC_002127.1 1330 bp DNA circular BCT 22-AUG-2022 -DEFINITION Escherichia coli o157:h7 Sakai plasmid pOSAK1, complete sequence. -ACCESSION NC_002127 -VERSION NC_002127.1 -KEYWORDS . -SOURCE Escherichia coli o157:h7 Sakai - ORGANISM Escherichia coli o157:h7 Sakai - . -COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 12:58:03 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 - CDSs :: 2 - tRNAs :: 0 - tmRNAs :: 0 - rRNAs :: 0 - ncRNAs :: 0 - regulatory ncRNAs :: 0 - CRISPR Arrays :: 0 - oriCs/oriVs :: 0 - oriTs :: 0 - gaps :: 0 -FEATURES Location/Qualifiers - source 1..1330 - /mol_type="genomic DNA" - /organism="Escherichia coli o157:h7 Sakai" - /strain="Sakai" - /plasmid="pOSAK1" - gene 413..736 - /locus_tag="IHHALP_00005" - CDS 413..736 - /product="hypothetical protein" - /locus_tag="IHHALP_00005" - /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA - AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL - MAD" - /codon_start=1 - /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00005" - /inference="ab initio prediction:Prodigal:2.6" - gene complement(join(971..1330,1..141)) - /locus_tag="IHHALP_00010" - CDS complement(join(971..1330,1..141)) - /product="hypothetical protein" - /locus_tag="IHHALP_00010" - /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA - EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR - YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG - IPI" - /codon_start=1 - /transl_table=11 - /protein_id="gnl|Bakta|IHHALP_00010" - /inference="ab initio prediction:Prodigal:2.6" -ORIGIN - 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc - 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc - 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg - 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt - 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt - 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac - 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa - 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga - 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt - 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga - 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga - 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag - 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt - 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga - 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc - 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc - 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa - 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat - 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat - 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa - 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc - 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg - 1321 cttctatttg -// |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.gff3 --- a/test-data/tmp/TEST_2/TEST_2.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,37 +0,0 @@ -##gff-version 3 -##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: v1.4.2 -# Database: v3.0 -# DOI: 10.1099/mgen.0.000685 -# URL: github.com/oschwengers/bakta -##sequence-region NC_002127.1 1 1330 -NC_002127.1 Bakta region 1 1330 . + . ID=NC_002127.1;Name=NC_002127.1;Is_circular=true -NC_002127.1 Prodigal CDS 413 736 . + 0 ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein -NC_002127.1 Prodigal CDS 971 1471 . - 0 ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein -##FASTA ->NC_002127.1 -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.hypotheticals.faa --- a/test-data/tmp/TEST_2/TEST_2.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.hypotheticals.tsv --- a/test-data/tmp/TEST_2/TEST_2.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta -#Database v3.0, 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 -NC_002127.1 971 141 - IHHALP_00010 18.9 7.7 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.json --- a/test-data/tmp/TEST_2/TEST_2.json Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,89 +0,0 @@ -{ - "genome": { - "genus": "Escherichia", - "species": "coli o157:h7", - "strain": "Sakai", - "plasmid": "pOSAK1", - "complete": true, - "gram": "?", - "translation_table": 11 - }, - "stats": { - "no_sequences": 1, - "size": 1330, - "gc": 0.4518796992481203, - "n_ratio": 0.0, - "n50": 1330, - "coding_ratio": 0.6203007518796992 - }, - "features": [ - { - "type": "cds", - "contig": "NC_002127.1", - "start": 413, - "stop": 736, - "strand": "+", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "GGAG/GAGG", - "db_xrefs": [], - "frame": 2, - "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", - "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", - "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 12072.90819999999, - "isoelectric_point": 10.367886161804197 - }, - "id": "IHHALPPJCH_1", - "locus": "IHHALP_00005" - }, - { - "type": "cds", - "contig": "NC_002127.1", - "start": 971, - "stop": 141, - "strand": "-", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "AGGA/GGAG/GAGG", - "db_xrefs": [], - "frame": 1, - "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", - "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", - "edge": true, - "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 18866.325799999995, - "isoelectric_point": 7.696590614318848 - }, - "id": "IHHALPPJCH_2", - "locus": "IHHALP_00010" - } - ], - "sequences": [ - { - "id": "NC_002127.1", - "description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", - "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", - "length": 1330, - "complete": true, - "type": "plasmid", - "topology": "circular", - "simple_id": "contig_1", - "name": "pOSAK1" - } - ], - "run": { - "start": "2022-08-22 12:58:02", - "end": "2022-08-22 12:58:03" - }, - "version": { - "bakta": "1.4.2", - "db": "3.0" - } -} \ No newline at end of file |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.log --- a/test-data/tmp/TEST_2/TEST_2.log Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,88 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - plasmids: 1 - -start annotation... -skip tRNA prediction... -skip tmRNA prediction... -predict rRNAs... - found: 0 -predict ncRNAs... - found: 0 -predict ncRNA regions... - found: 0 -predict CRISPR arrays... - found: 0 -predict & annotate CDSs... - predicted: 2 - discarded spurious: 0 - revised translational exceptions: 0 - detected IPSs: 0 - found PSCs: 0 - found PSCCs: 0 - lookup annotations... - conduct expert systems... - amrfinder: 0 - protein sequences: 0 - combine annotations and mark hypotheticals... - analyze hypothetical proteins: 2 - detected Pfam hits: 0 - calculated proteins statistics - revise special cases... -extract sORF... - potential: 22 - discarded due to overlaps: 2 - discarded spurious: 0 - detected IPSs: 0 - found PSCs: 0 - lookup annotations... - filter and combine annotations... - filtered sORFs: 0 -detect gaps... - found: 0 -detect oriCs/oriVs... - found: 0 -detect oriTs... - found: 0 -apply feature overlap filters... -select features and create locus tags... -selected: 2 - -genome statistics: - Genome size: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - N ratio: 0.0 % - coding density: 62.0 % - -annotation summary: - tRNAs: 0 - tmRNAs: 0 - rRNAs: 0 - ncRNAs: 0 - ncRNA regions: 0 - CRISPR arrays: 0 - CDSs: 2 - hypotheticals: 2 - signal peptides: 0 - sORFs: 0 - gaps: 0 - oriCs/oriVs: 0 - oriTs: 0 - -export annotation results to: /tmp/tmpqcic3cc5/job_working_directory/000/4/working - human readable TSV... - GFF3... - INSDC GenBank & EMBL... - genome sequences... - feature nucleotide sequences... - translated CDS sequences... - 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]. |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.tsv --- a/test-data/tmp/TEST_2/TEST_2.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): 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 -NC_002127.1 cds 971 141 - IHHALP_00010 hypothetical protein |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_2/TEST_2.txt --- a/test-data/tmp/TEST_2/TEST_2.txt Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,29 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 62.0 - -Annotation: -tRNAs: 0 -tmRNAs: 0 -rRNAs: 0 -ncRNAs: 0 -ncRNA regions: 0 -CRISPR arrays: 0 -CDSs: 2 -hypotheticals: 2 -signal peptides: 0 -sORFs: 0 -gaps: 0 -oriCs: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.4.2 -Database: v3.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.embl --- a/test-data/tmp/TEST_3/TEST_3.embl Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,62 +0,0 @@ -ID contig_1; ; circular; DNA; ; PRO; 1330 BP. -XX -AC contig_1; -XX -DE plasmid unnamed1, complete sequence -XX -OS . -OC . -XX -CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 08/22/2022, 12:58:17 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 -CC CDSs :: 0 -CC tRNAs :: 0 -CC tmRNAs :: 0 -CC rRNAs :: 0 -CC ncRNAs :: 0 -CC regulatory ncRNAs :: 0 -CC CRISPR Arrays :: 0 -CC oriCs/oriVs :: 0 -CC oriTs :: 0 -CC gaps :: 0 -XX -FH Key Location/Qualifiers -FH -FT source 1..1330 -FT /mol_type="genomic DNA" -FT /plasmid="unnamed1" -XX -SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; - ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 - gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 - agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 - tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 - tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 - gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 - cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 - acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 - agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 - acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 - agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 - cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 - gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 - aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 - tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 - agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 - tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 - ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 - cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 - taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 - aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 - tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 - cttctatttg 1330 -// |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.fna --- a/test-data/tmp/TEST_3/TEST_3.fna Thu Sep 01 17:28:43 2022 +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 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.gbff --- a/test-data/tmp/TEST_3/TEST_3.gbff Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,58 +0,0 @@ -LOCUS contig_1 1330 bp DNA circular BCT 22-AUG-2022 -DEFINITION plasmid unnamed1, complete sequence. -ACCESSION contig_1 -VERSION contig_1 -KEYWORDS . -SOURCE None - ORGANISM . - . -COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 12:58:17 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 - CDSs :: 0 - tRNAs :: 0 - tmRNAs :: 0 - rRNAs :: 0 - ncRNAs :: 0 - regulatory ncRNAs :: 0 - CRISPR Arrays :: 0 - oriCs/oriVs :: 0 - oriTs :: 0 - gaps :: 0 -FEATURES Location/Qualifiers - source 1..1330 - /mol_type="genomic DNA" - /plasmid="unnamed1" -ORIGIN - 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc - 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc - 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg - 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt - 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt - 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac - 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa - 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga - 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt - 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga - 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga - 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag - 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt - 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga - 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc - 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc - 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa - 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat - 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat - 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa - 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc - 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg - 1321 cttctatttg -// |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.gff3 --- a/test-data/tmp/TEST_3/TEST_3.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,34 +0,0 @@ -##gff-version 3 -##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo -# Annotated with Bakta -# Software: v1.4.2 -# Database: v3.0 -# DOI: 10.1099/mgen.0.000685 -# URL: github.com/oschwengers/bakta -##sequence-region contig_1 1 1330 -contig_1 Bakta region 1 1330 . + . ID=contig_1;Name=contig_1;Is_circular=true -##FASTA ->contig_1 -TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC -GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC -AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG -TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT -TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT -GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC -CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA -ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA -AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT -ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA -AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA -CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG -GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT -AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA -TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC -AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC -TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA -GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT -CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT -TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA -AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC -TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG -CTTCTATTTG |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.json --- a/test-data/tmp/TEST_3/TEST_3.json Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,42 +0,0 @@ -{ - "genome": { - "genus": null, - "species": null, - "strain": null, - "complete": true, - "gram": "?", - "translation_table": 11 - }, - "stats": { - "no_sequences": 1, - "size": 1330, - "gc": 0.4518796992481203, - "n_ratio": 0.0, - "n50": 1330, - "coding_ratio": 0.0 - }, - "features": [], - "sequences": [ - { - "id": "contig_1", - "description": "[completeness=complete] [topology=circular] [gcode=11]", - "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", - "length": 1330, - "complete": true, - "type": "plasmid", - "topology": "circular", - "simple_id": "contig_1", - "orig_id": "NC_002127.1", - "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", - "name": "unnamed1" - } - ], - "run": { - "start": "2022-08-22 12:58:17", - "end": "2022-08-22 12:58:17" - }, - "version": { - "bakta": "1.4.2", - "db": "3.0" - } -} \ No newline at end of file |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.log --- a/test-data/tmp/TEST_3/TEST_3.log Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,55 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - 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: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - 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: /tmp/tmpqcic3cc5/job_working_directory/000/6/working - 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]. |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.tsv --- a/test-data/tmp/TEST_3/TEST_3.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): https://doi.org/10.5281/zenodo.4247252 -#Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_3/TEST_3.txt --- a/test-data/tmp/TEST_3/TEST_3.txt Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,29 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 0.0 - -Annotation: -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: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.4.2 -Database: v3.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.embl --- a/test-data/tmp/TEST_4/TEST_4.embl Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,87 +0,0 @@ -ID p2; ; circular; DNA; ; PRO; 1330 BP. -XX -AC p2; -XX -DE plasmid pOSAK1, complete sequence -XX -OS . -OC . -XX -CC Annotated with Bakta -CC Software: v1.4.2 -CC Database: v3.0 -CC DOI: 10.1099/mgen.0.000685 -CC URL: github.com/oschwengers/bakta -CC -CC ##Genome Annotation Summary:## -CC Annotation Date :: 08/22/2022, 12:58:56 -CC Annotation Pipeline :: Bakta -CC Annotation Software version :: v1.4.2 -CC Annotation Database version :: v3.0 -CC CDSs :: 2 -CC tRNAs :: 0 -CC tmRNAs :: 0 -CC rRNAs :: 0 -CC ncRNAs :: 0 -CC regulatory ncRNAs :: 0 -CC CRISPR Arrays :: 0 -CC oriCs/oriVs :: 0 -CC oriTs :: 0 -CC gaps :: 0 -XX -FH Key Location/Qualifiers -FH -FT source 1..1330 -FT /mol_type="genomic DNA" -FT /plasmid="pOSAK1" -FT gene 413..736 -FT /locus_tag="IHHALP_00005" -FT CDS 413..736 -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00005" -FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA -FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL -FT MAD" -FT /codon_start=1 -FT /transl_table=4 -FT /protein_id="gnl|Bakta|IHHALP_00005" -FT /inference="ab initio prediction:Prodigal:2.6" -FT gene complement(join(971..1330,1..141)) -FT /locus_tag="IHHALP_00010" -FT CDS complement(join(971..1330,1..141)) -FT /product="hypothetical protein" -FT /locus_tag="IHHALP_00010" -FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA -FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR -FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG -FT IPI" -FT /codon_start=1 -FT /transl_table=4 -FT /protein_id="gnl|Bakta|IHHALP_00010" -FT /inference="ab initio prediction:Prodigal:2.6" -XX -SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other; - ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc 60 - gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc 120 - agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg 180 - tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt 240 - tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt 300 - gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac 360 - cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa 420 - acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga 480 - agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt 540 - acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga 600 - agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga 660 - cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag 720 - gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt 780 - aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga 840 - tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc 900 - agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc 960 - tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa 1020 - ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat 1080 - cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat 1140 - taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa 1200 - aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc 1260 - tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg 1320 - cttctatttg 1330 -// |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.faa --- a/test-data/tmp/TEST_4/TEST_4.faa Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.ffn --- a/test-data/tmp/TEST_4/TEST_4.ffn Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG ->IHHALP_00010 hypothetical protein -ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.fna --- a/test-data/tmp/TEST_4/TEST_4.fna Thu Sep 01 17:28:43 2022 +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 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.gbff --- a/test-data/tmp/TEST_4/TEST_4.gbff Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,83 +0,0 @@ -LOCUS p2 1330 bp DNA circular BCT 22-AUG-2022 -DEFINITION plasmid pOSAK1, complete sequence. -ACCESSION p2 -VERSION p2 -KEYWORDS . -SOURCE None - ORGANISM . - . -COMMENT Annotated with Bakta - Software: v1.4.2 - Database: v3.0 - DOI: 10.1099/mgen.0.000685 - URL: github.com/oschwengers/bakta - - ##Genome Annotation Summary:## - Annotation Date :: 08/22/2022, 12:58:56 - Annotation Pipeline :: Bakta - Annotation Software version :: v1.4.2 - Annotation Database version :: v3.0 - CDSs :: 2 - tRNAs :: 0 - tmRNAs :: 0 - rRNAs :: 0 - ncRNAs :: 0 - regulatory ncRNAs :: 0 - CRISPR Arrays :: 0 - oriCs/oriVs :: 0 - oriTs :: 0 - gaps :: 0 -FEATURES Location/Qualifiers - source 1..1330 - /mol_type="genomic DNA" - /plasmid="pOSAK1" - gene 413..736 - /locus_tag="IHHALP_00005" - CDS 413..736 - /product="hypothetical protein" - /locus_tag="IHHALP_00005" - /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA - AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL - MAD" - /codon_start=1 - /transl_table=4 - /protein_id="gnl|Bakta|IHHALP_00005" - /inference="ab initio prediction:Prodigal:2.6" - gene complement(join(971..1330,1..141)) - /locus_tag="IHHALP_00010" - CDS complement(join(971..1330,1..141)) - /product="hypothetical protein" - /locus_tag="IHHALP_00010" - /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA - EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR - YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG - IPI" - /codon_start=1 - /transl_table=4 - /protein_id="gnl|Bakta|IHHALP_00010" - /inference="ab initio prediction:Prodigal:2.6" -ORIGIN - 1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc - 61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc - 121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg - 181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt - 241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt - 301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac - 361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa - 421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga - 481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt - 541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga - 601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga - 661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag - 721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt - 781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga - 841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc - 901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc - 961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa - 1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat - 1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat - 1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa - 1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc - 1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg - 1321 cttctatttg -// |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.gff3 --- a/test-data/tmp/TEST_4/TEST_4.gff3 Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -##gff-version 3 -##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo -# Annotated with Bakta -# Software: v1.4.2 -# Database: v3.0 -# DOI: 10.1099/mgen.0.000685 -# URL: github.com/oschwengers/bakta -##sequence-region p2 1 1330 -p2 Bakta region 1 1330 . + . ID=p2;Name=p2;Is_circular=true -p2 Prodigal gene 413 736 . + . ID=IHHALP_00005_gene;locus_tag=IHHALP_00005 -p2 Prodigal CDS 413 736 . + 0 ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein;Parent=IHHALP_00005_gene;inference=ab initio prediction:Prodigal:2.6 -p2 Prodigal gene 971 1471 . - . ID=IHHALP_00010_gene;locus_tag=IHHALP_00010 -p2 Prodigal CDS 971 1471 . - 0 ID=IHHALP_00010;Name=hypothetical protein;locus_tag=IHHALP_00010;product=hypothetical protein;Parent=IHHALP_00010_gene;inference=ab initio prediction:Prodigal:2.6 |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.hypotheticals.faa --- a/test-data/tmp/TEST_4/TEST_4.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->IHHALP_00005 hypothetical protein -MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD ->IHHALP_00010 hypothetical protein -MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.hypotheticals.tsv --- a/test-data/tmp/TEST_4/TEST_4.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta -#Database v3.0, 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 -p2 971 141 - IHHALP_00010 18.9 7.7 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.json --- a/test-data/tmp/TEST_4/TEST_4.json Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,89 +0,0 @@ -{ - "genome": { - "genus": null, - "species": null, - "strain": null, - "complete": true, - "gram": "?", - "translation_table": 4 - }, - "stats": { - "no_sequences": 1, - "size": 1330, - "gc": 0.4518796992481203, - "n_ratio": 0.0, - "n50": 1330, - "coding_ratio": 0.6203007518796992 - }, - "features": [ - { - "type": "cds", - "contig": "p2", - "start": 413, - "stop": 736, - "strand": "+", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "GGAG/GAGG", - "db_xrefs": [], - "frame": 2, - "aa": "MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD", - "aa_hexdigest": "d9bdebc84195542e775c3d22458b507e", - "nt": "ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 12072.90819999999, - "isoelectric_point": 10.367886161804197 - }, - "id": "IHHALPPJCH_1", - "locus": "IHHALP_00005" - }, - { - "type": "cds", - "contig": "p2", - "start": 971, - "stop": 141, - "strand": "-", - "gene": null, - "product": "hypothetical protein", - "start_type": "ATG", - "rbs_motif": "AGGA/GGAG/GAGG", - "db_xrefs": [], - "frame": 1, - "aa": "MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI", - "aa_hexdigest": "1e7027cbe48346e06a83e802a9385584", - "edge": true, - "nt": "ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA", - "hypothetical": true, - "seq_stats": { - "molecular_weight": 18866.325799999995, - "isoelectric_point": 7.696590614318848 - }, - "id": "IHHALPPJCH_2", - "locus": "IHHALP_00010" - } - ], - "sequences": [ - { - "id": "p2", - "description": "[completeness=complete] [topology=circular] [gcode=4] [plasmid-name=pOSAK1]", - "sequence": "TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGCGTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGCAGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTGTGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATTTCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTTGCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTACCCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGTAAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGATCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTCAGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTCTGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAAGGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAATCATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCATTAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAAAAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGCTCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTGCTTCTATTTG", - "length": 1330, - "complete": true, - "type": "plasmid", - "topology": "circular", - "orig_id": "NC_002127.1", - "orig_description": "Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence", - "name": "pOSAK1" - } - ], - "run": { - "start": "2022-08-22 12:58:54", - "end": "2022-08-22 12:58:56" - }, - "version": { - "bakta": "1.4.2", - "db": "3.0" - } -} \ No newline at end of file |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.log --- a/test-data/tmp/TEST_4/TEST_4.log Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,91 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - plasmids: 1 - -start annotation... -predict tRNAs... - found: 0 -predict tmRNAs... - found: 0 -predict rRNAs... - found: 0 -predict ncRNAs... - found: 0 -predict ncRNA regions... - found: 0 -predict CRISPR arrays... - found: 0 -predict & annotate CDSs... - predicted: 2 - discarded spurious: 0 - revised translational exceptions: 0 - detected IPSs: 0 - found PSCs: 0 - found PSCCs: 0 - lookup annotations... - conduct expert systems... - amrfinder: 0 - protein sequences: 0 - user protein sequences: 0 - combine annotations and mark hypotheticals... - analyze hypothetical proteins: 2 - detected Pfam hits: 0 - calculated proteins statistics - revise special cases... -extract sORF... - potential: 16 - discarded due to overlaps: 2 - discarded spurious: 0 - detected IPSs: 0 - found PSCs: 0 - lookup annotations... - filter and combine annotations... - filtered sORFs: 0 -detect gaps... - found: 0 -detect oriCs/oriVs... - found: 0 -detect oriTs... - found: 0 -apply feature overlap filters... -select features and create locus tags... -selected: 2 - -genome statistics: - Genome size: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - N ratio: 0.0 % - coding density: 62.0 % - -annotation summary: - tRNAs: 0 - tmRNAs: 0 - rRNAs: 0 - ncRNAs: 0 - ncRNA regions: 0 - CRISPR arrays: 0 - CDSs: 2 - hypotheticals: 2 - signal peptides: 0 - sORFs: 0 - gaps: 0 - oriCs/oriVs: 0 - oriTs: 0 - -export annotation results to: /tmp/tmpqcic3cc5/job_working_directory/000/12/working - human readable TSV... - GFF3... - INSDC GenBank & EMBL... - genome sequences... - feature nucleotide sequences... - translated CDS sequences... - 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]. |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.tsv --- a/test-data/tmp/TEST_4/TEST_4.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta -#Database (v3.0): 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 -p2 cds 971 141 - IHHALP_00010 hypothetical protein |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_4/TEST_4.txt --- a/test-data/tmp/TEST_4/TEST_4.txt Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,29 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 62.0 - -Annotation: -tRNAs: 0 -tmRNAs: 0 -rRNAs: 0 -ncRNAs: 0 -ncRNA regions: 0 -CRISPR arrays: 0 -CDSs: 2 -hypotheticals: 2 -signal peptides: 0 -sORFs: 0 -gaps: 0 -oriCs: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.4.2 -Database: v3.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_5/TEST_5.log --- a/test-data/tmp/TEST_5/TEST_5.log Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,55 +0,0 @@ -parse genome sequences... - imported: 1 - filtered & revised: 1 - 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: 1,330 bp - Contigs/replicons: 1 - GC: 45.2 % - N50: 1,330 - 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: /tmp/tmpqcic3cc5/job_working_directory/000/14/working - 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]. |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/TEST_5/TEST_5.txt --- a/test-data/tmp/TEST_5/TEST_5.txt Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,29 +0,0 @@ -Sequence(s): -Length: 1330 -Count: 1 -GC: 45.2 -N50: 1330 -N ratio: 0.0 -coding density: 0.0 - -Annotation: -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: 0 -oriVs: 0 -oriTs: 0 - -Bakta: -Software: v1.4.2 -Database: v3.0 -DOI: 10.1099/mgen.0.000685 -URL: github.com/oschwengers/bakta |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/prodigal.tf |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/replicons.tsv --- a/test-data/tmp/replicons.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -NC_002695.2 c1 c c - -NC_002128.1 p1 plasmid c pO157 -NC_002127.1 p2 p c pOSAK1 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab --- a/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#taxgroup accession_version mutation_position mutation_symbol class subclass mutated_protein_name -Escherichia WP_000019358.1 12 soxS_A12S MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE Escherichia_ampicillin/chloramphenicol/quinolone/rifampin/tetracycline_resistant_SoxS |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress --- a/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#taxgroup protein_accession protein_gi -Escherichia AAA21095.1 151858 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab --- a/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#taxgroup gene_symbol accession_version resistance_cutoff class subclass resistance_protein_name -Streptococcus_pneumoniae pbp1a WP_001040013.1 99.000000 BETA-LACTAM BETA-LACTAM Streptococcus_pneumoniae_beta-lactam_resistant_PBP1A |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt --- a/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -3.10.16 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/fam.tab --- a/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/fam.tab Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1744 +0,0 @@\n-#node_id\tparent_node_id\tgene_symbol\thmm_id\thmm_tc1\thmm_tc2\tblastrule_complete_ident\tblastrule_complete_wp_coverage\tblastrule_complete_br_coverage\tblastrule_partial_ident\tblastrule_partial_wp_coverage\tblastrule_partial_br_coverage\treportable\ttype\tsubtype\tclass\tsubclass\tfamily_name\n-ACID\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tACID\t\t\t\n-ALL\t\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\t\t\t\t\t\n-AME\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\taminoglycoside modifying enzymes\n-AMR\tALL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\t\n-BIOCIDE\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tBIOCIDE\t\t\t\n-BcII\tbla-B1\tbla2\tNF033095.1\t500.00\t500.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tCARBAPENEM\tBcII family subclass B1 metallo-beta-lactamase\n-CDF_efflux\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tCDF family cation efflux transporter\n-CMY2-MIR-ACT-EC\tbla-C\tampC\tNF012173.1\t680.00\t680.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBETA-LACTAM\tBETA-LACTAM\tCMY2/MIR/ACT/EC family class C beta-lactamase\n-EFFLUX\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tefflux\n-HARLDQ_not_B3\tbla-B3\t-\tNF000405.1\t350.00\t350.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tHARLDQ motif MBL-fold protein\n-HEAT\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tHEAT\t\t\t\n-HTH_5\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tArsR/SmtB family metalloregulatory transcriptional repressor\n-LHR_hdeD\tHEAT\thdeD-GI\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t93.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance membrane protein HdeD-GI\n-LHR_hsp20A\tHEAT\thsp20\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20\n-LHR_hsp20B\tHEAT\tshsP\t-\t0.00\t0.00\t93.00\t90.00\t90.00\t94.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\tsmall heat shock protein sHSP20-GI\n-LHR_kefB\tHEAT\tkefB-GI\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system K+/H+ antiporter KefB-GI\n-LHR_psiE\tHEAT\tpsi-GI\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein PsiE-GI\n-LHR_trx\tHEAT\ttrxLHR\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance system thioredoxin Trx-GI\n-LHR_yfdX1\tHEAT\tyfdX1\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX1\n-LHR_yfdX2\tHEAT\tyfdX2\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t90.00\t90.00\t25.00\t1\tSTRESS\tHEAT\t\t\theat resistance protein YfdX2\n-MATE_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MATE transporter\n-METAL-RND-IM\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tcation efflux RND transporter permease subunit\n-METAL\tSTRESS\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tMetal Resistance\n-MFS_efflux_CHL\tMFS_efflux\tcml\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tPHENICOL\tCHLORAMPHENICOL\tchloramphenicol efflux MFS transporter\n-MFS_efflux_qac\tBIOCIDE\tqac\tNF000089.1\t900.00\t900.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tSTRESS\tBIOCIDE\tQUATERNARY AMMONIUM\tQUATERNARY AMMONIUM\tQacA/B family quaternary ammonium compound efflux MFS transporter\n-MFS_efflux\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux MFS transporter\n-MerP_Gneg\tmerP\tmerP\tTIGR02052.1\t92.55\t92.55\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t1\tSTRESS\tMETAL\tMERCURY\tMERCURY\tmercury resistance system periplasmic binding protein MerP\n-OM_sidero\tVIRULENCE_Ecoli\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tVIRULENCE\tVIRULENCE\t\t\tTonB-dependent siderophore receptor\n-P-type_ATPase\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tmetal-translocating P-type ATPase\n-PERI-SENSOR\tMETAL\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tSTRESS\tMETAL\t\t\tperiplasmic heavy metal sensor\n-RESPONSE_REG\tAMR\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tDNA-binding response regulator\n-RND-IM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug efflux RND transporter permease subunit\n-RND-OM\tEFFLUX\t-\t-\t0\t0\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0\tAMR\tAMR\t\t\tmultidrug'..b'ferase Vat(A)\n-vat(B)\tvat\tvat(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(B)\n-vat(C)\tvat\tvat(C)\tNF000097.1\t425.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(C)\n-vat(D)\tvat\tvat(D)\tNF000111.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(D)\n-vat(E)\tvat\tvat(E)\tNF000020.1\t450.00\t450.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(E)\n-vat(F)\tvat\tvat(F)\tNF000147.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(F)\n-vat(H)\tvat\tvat(H)\tNF000504.1\t475.00\t425.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(H)\n-vat(I)\tvat\tvatI\tNF033468.1\t415.00\t415.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin A O-acetyltransferase Vat(I)\n-vat\tAMR\tvat\tNF000311.1\t300.00\t300.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tVat family streptogramin A O-acetyltransferase\n-vga(A)\tvga\tvga(A)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(A)\n-vga(B)\tvga\tvga(B)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(B)\n-vga(C)\tvga\tvga(C)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(C)\n-vga(D)\tvga\tvga(D)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(D)\n-vga(E)\tvga\tvga(E)\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tABC-F type ribosomal protection protein Vga(E)\n-vga\tabc-f\tvga\tNF000170.1\t800.00\t800.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tLINCOSAMIDE\tLINCOSAMIDE\tVga family ABC-F type ribosomal protection protein\n-vgb(A)\tvgb\tvgb(A)\tNF000022.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(A)\n-vgb(B)\tvgb\tvgb(B)\tNF000096.1\t600.00\t600.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(B)\n-vgb(C)\tvgb\tvgbC\t-\t0.00\t0.00\t84.00\t90.00\t90.00\t88.00\t90.00\t25.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase Vgb(C)\n-vgb\tAMR\tvgb\t-\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tSTREPTOGRAMIN\tSTREPTOGRAMIN\tstreptogramin B lyase\n-virF\tVIRULENCE_Ecoli\tvirF\t-\t0.00\t0.00\t94.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tAraC family invasion system transcriptional regulator VirF\n-vmlR\tabc-f\tvmlR\t-\t0.00\t0.00\t90.00\t90.00\t90.00\t96.00\t90.00\t25.00\t2\tAMR\tAMR\tMACROLIDE/PLEUROMUTILIN\tLINCOSAMIDE/STREPTOGRAMIN/TIAMULIN\tABC-F type ribosomal protection protein VmlR\n-vph\tAMR\tvph\tNF000088.1\t400.00\t400.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tTUBERACTINOMYCIN\tVIOMYCIN\tviomycin phosphotransferase\n-ybtP\tVIRULENCE\tybtP\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtP\n-ybtQ\tVIRULENCE\tybtQ\t-\t0.00\t0.00\t85.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tyersiniabactin ABC transporter ATP-binding/permease protein YbtQ\n-yfeA\tVIRULENCE\tyfeA\t-\t0.00\t0.00\t83.00\t90.00\t90.00\t88.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter substrate-binding protein YfeA\n-yfeB\tVIRULENCE\tyfeB\t-\t0.00\t0.00\t86.00\t90.00\t90.00\t96.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter ATP-binding protein YfeB\n-yfeD\tVIRULENCE\tyfeD\t-\t0.00\t0.00\t88.00\t90.00\t90.00\t92.00\t90.00\t25.00\t1\tVIRULENCE\tVIRULENCE\t\t\tiron/manganese ABC transporter permease subunit YfeD\n-zbmA\tble\tzbmA\tNF000479.1\t280.00\t280.00\t0.00\t0.00\t0.00\t0.00\t0.00\t0.00\t2\tAMR\tAMR\tBLEOMYCIN\tZORBAMYCIN\tzorbamycin binding protein ZbmA\n' |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab --- a/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#taxgroup gpipe_taxgroup number_of_nucl_ref_genes -Acinetobacter_baumannii Acinetobacter 0 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/version.txt --- a/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/version.txt Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -2021-09-30.1 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/antifam.h3f |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/bakta.db |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/expert-protein-sequences.dmnd |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/ncRNA-genes.i1f |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/oric.fna --- a/test-data/tmp/test-db/oric.fna Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->ORI10010001 -TATTCTTCTATAACATTGTCAAGAATGATAGTTAAAATTCTCGAAATTGGGATATTAACTGCTTTGGAGTAATTTCTAACTTTTTGTCATACTCTTTGACTTGTATAGAAGTGTACACCTGTATCTAGTTTTTCTTGGCGTTCAACAGGAACTATTCCTGGTATTTTTGTTTTAGGTTGGGGAGGAATAGGCTGTGGTTGTGTGAATTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATGATATTGAAAATTTTGTTCCTCTTGAAAATATCTCTCTTTTTTTGGTTTTCCAGAAAAATTTGATGAAAAAGATTTTTCTTCATTTCAATTTTCAAGATTATTTTCATTTTGTTGATTTATTTGCTCAGGCTGTTGAAATGAATTATTTTTTGATCAAAAAGATTTTGGAAAGGTTTTTTCAAAAGCAGATAAAGGTCCAAAATCAAATGAAGATGAATCTTTGTCAAAAGATGTTTCTTCTCTTTTTGACAAATTTTGTTTTTGATTAAACTTATTTTTATTTTGGGGTGTTACTTTTTCTTTTATGGAAAACAAATCTTCTTCTAAAAGACTTTGTTCTGGGTCATCATCTTGTGCTAAATCAAAGAAAAAACGTTTCTTTTTGTTA ->ORI10010003 -GGCGTAGACACTGAATTCGATGGGGATAAGTGGTGGATAAAAGAATATAAATTAGTCATTACACTTTACTCACGAATATCCCCCTTTTTTTAGAGAAAAAATATACTTTCTTCACAAGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCGAGACATAAGCACTTATCCAGATATTCACAGTTACTATTATGTGATACGACTACATTCTTTATACTTATAAGATTAATAAGGAGGAAACTAACT |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/orit.fna --- a/test-data/tmp/test-db/orit.fna Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->CP019995|MOBP -GTAGAATCGTTTAGTATGAGAATAGAAAACCAACGGTTTTCATGAACTTACTAAACGATTCTAC ->CP012386|MOBP -AGAACAATCAACAACTAATTAGGCAAATTAAGGGGTGCTAAACAACTGCTAGTAGGTGCTAGAGATGTGCTATAAAGGGTGCTAGTTTGGTGCTAGTTACTGCTAAATACGTGCTAGTTTAGGTGCTAGAAACGTGCTATATGGTGCTAAAAAGGTGCTAGTTTGCATGAAGTTACCTGCTAGCCAAGTGCTAGTGGCGTTCGTTTTTGGGTCCCACGGGAAAGCCTTGCACTGCAAGGCGGGTCAGCTTGTCTGACCCCCATTTCCCCTTATGCTCTTCCGAAACACAAAGCGCAATTAAGCGAATACTAGAGAATAAATA |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/pfam.h3f |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/rRNA.i1f |
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| Binary file test-data/tmp/test-db/rRNA.i1m has changed |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/rfam-go.tsv --- a/test-data/tmp/test-db/rfam-go.tsv Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -Rfam:RF00001 GO:0003735 |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/sorf.dmnd |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test-db/version.json --- a/test-data/tmp/test-db/version.json Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,53 +0,0 @@ -{ - "date": "2021-08-9", - "major": 3, - "minor": 0, - "dependencies": [ - { - "name": "AMRFinderPlus", - "release": "2020-09-22.2" - }, - { - "name": "COG", - "release": "2014" - }, - { - "name": "DoriC", - "release": "10" - }, - { - "name": "ISFinder", - "release": "2019-09-25" - }, - { - "name": "Mob-suite", - "release": "2.0" - }, - { - "name": "Pfam", - "release": "33.1" - }, - { - "name": "RefSeq", - "release": "r202" - }, - { - "name": "Rfam", - "release": "14.2" - }, - { - "name": "UniProtKB/Swiss-Prot", - "release": "2020_04" - } - ], - "experts": [ - { - "name": "AMRFinderPlus", - "release": "3.10.1" - }, - { - "name": "NCBI BlastRules", - "release": "4.0" - } - ] -} |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/test_database.loc --- a/test-data/tmp/test_database.loc Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -# Tab separated with 4 columns: -# - value (Galaxy records this in the Galaxy DB) -# - name (Galaxy shows this in the UI) -# - path (folder name containing the NCBI DB) -test-db-bakta "Database test" ${__HERE__}/test-db |
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| diff -r 1a27ad3d0cdf -r da5f1924bb2e test-data/tmp/user-proteins.faa --- a/test-data/tmp/user-proteins.faa Thu Sep 01 17:28:43 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->VFDB_test 90~~~90~~~90~~~yaxA~~~cytotoxin YaxA~~~VFDB:VFG045347,VFDB:VF0511,EC:1.1.1.1,EC:2.2.2.2 -MTQTQLAIDNVLASAENTIQLNELPKVVLDFITGEQTSVARSGGIFTKEDLINLKLYVRKGLSLPTRQDEVEAYLGYKKIDVAGLEPKDIKLLFDEIHNHALNWNDVEQAVLQQSLDLDIAAKNIISTGNEIINLINQMPITLRVKTLLRDITDKQLENITYESADHEVASALKDILDDMKGDINRHQTTTENVRKKVSDYRITLTGGELSSGDKVNGLEPQVKTKYDLMEKSNMRKSIKELDEKIKEKKQRIEQLKKDYDKFVGLSFTGAIGGIIAMAITSGIFGAKAENARKEKNALISEVAELESKVSSQRALQTALEALSLSFSDIGIRMVDAESALNHLDFMWLSVLNQITESQIQFAMINNALRLTSFVNKFQQVITPWQSVGDSARQLVDIFDEAIKEYKKVYG ->hypo-mock-test 99~~~99~~~99~~~mock1~~~mock hypothetical user protein 1~~~USERDB:MOCK1,EC:0.0.0.0 -MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYKGIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDRANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIASLINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSLIMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREIHQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGGVARLKL \ No newline at end of file |