| Next changeset 1:da5f1924bb2e (2022-09-16) |
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Commit message:
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3 |
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added:
bakta.xml macro.xml test-data/NC_002127.1.fna test-data/TEST_1/TEST_1.embl test-data/TEST_1/TEST_1.faa test-data/TEST_1/TEST_1.ffn test-data/TEST_1/TEST_1.fna test-data/TEST_1/TEST_1.gbff test-data/TEST_1/TEST_1.gff3 test-data/TEST_1/TEST_1.hypotheticals.faa 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.faa test-data/TEST_2/TEST_2.ffn test-data/TEST_2/TEST_2.fna test-data/TEST_2/TEST_2.gbff test-data/TEST_2/TEST_2.gff3 test-data/TEST_2/TEST_2.hypotheticals.faa 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.faa test-data/TEST_3/TEST_3.ffn test-data/TEST_3/TEST_3.fna 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.faa test-data/TEST_4/TEST_4.ffn test-data/TEST_4/TEST_4.fna test-data/TEST_4/TEST_4.gbff test-data/TEST_4/TEST_4.gff3 test-data/TEST_4/TEST_4.hypotheticals.faa 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/prodigal.tf test-data/replicons.tsv test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pdb test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.phr test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pin test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.psq test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.ptf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pto test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.not test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto test-data/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt test-data/test-db/amrfinderplus-db/2021-09-30.1/fam.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab test-data/test-db/amrfinderplus-db/2021-09-30.1/version.txt test-data/test-db/antifam.h3f test-data/test-db/antifam.h3i test-data/test-db/antifam.h3m test-data/test-db/antifam.h3p test-data/test-db/bakta.db test-data/test-db/expert-protein-sequences.dmnd test-data/test-db/ncRNA-genes.i1f test-data/test-db/ncRNA-genes.i1i test-data/test-db/ncRNA-genes.i1m test-data/test-db/ncRNA-genes.i1p test-data/test-db/ncRNA-regions.i1f test-data/test-db/ncRNA-regions.i1i test-data/test-db/ncRNA-regions.i1m test-data/test-db/ncRNA-regions.i1p test-data/test-db/oric.fna test-data/test-db/orit.fna test-data/test-db/pfam.h3f test-data/test-db/pfam.h3i test-data/test-db/pfam.h3m test-data/test-db/pfam.h3p test-data/test-db/psc.dmnd test-data/test-db/rRNA.i1f test-data/test-db/rRNA.i1i test-data/test-db/rRNA.i1m test-data/test-db/rRNA.i1p test-data/test-db/rfam-go.tsv test-data/test-db/sorf.dmnd test-data/test-db/version.json test-data/test_database.loc 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 test-data/user-proteins.faa tool-data/bakta_database.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 1a27ad3d0cdf bakta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bakta.xml Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| b'@@ -0,0 +1,507 @@\n+<tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>\n+ genome annotation via alignment-free sequence identification\n+ </description>\n+ <macros>\n+ <import>macro.xml</import>\n+ </macros>\n+ <expand macro=\'edam\'/>\n+ <expand macro=\'xrefs\'/>\n+ <expand macro="requirements"/>\n+ <expand macro="version_command"/>\n+\n+ <command detect_errors="aggressive"><![CDATA[\n+ bakta\n+ #*======================================\n+ CPU option\n+ ======================================*#\n+ --threads \\${GALAXY_SLOTS:-1}\n+ #*======================================\n+ Bakta database\n+ ======================================*#\n+ --db $input_option.db_select.fields.path\n+ #if $input_option.min_contig_length\n+ --min-contig-length $input_option.min_contig_length\n+ #else if $annotation.compliant\n+ --min-contig-length 200\n+ #else\n+ --min-contig-length 1\n+ #end if\n+ --prefix bakta_output\n+ #*======================================\n+ Organism options\n+ genus/species/strain/plasmid\n+ ======================================*#\n+ #if $organism.genus\n+ --genus \'$organism.genus\'\n+ #end if\n+ #if $organism.species\n+ --species \'$organism.species\'\n+ #end if\n+ #if $organism.strain\n+ --strain \'$organism.strain\'\n+ #end if\n+ #if $organism.plasmid\n+ --plasmid \'$organism.plasmid\'\n+ #end if\n+ #*======================================\n+ Annotation options\n+ gram type, prodigal/protein file\n+ ======================================*#\n+ $annotation.complete\n+ #if $annotation.prodigal\n+ --prodigal-tf \'$annotation.prodigal\'\n+ #end if\n+ #if $annotation.translation_table\n+ --translation-table \'$annotation.translation_table\'\n+ #end if\n+ #if $annotation.gram\n+ --gram \'$annotation.gram\'\n+ #end if\n+ $annotation.keep_contig_headers\n+ #if $annotation.replicons\n+ --replicons \'$annotation.replicons\'\n+ #end if\n+ $annotation.compliant\n+ #if $annotation.proteins\n+ --proteins \'$annotation.proteins\'\n+ #end if\n+ #*======================================\n+ Workflow OPTIONS\n+ skip some step of the bakta analysis\n+ ======================================*#\n+\n+ #if "skip_trna" in $workflow.skip_analysis\n+ --skip-trna\n+ #end if\n+ #if "skip_tmrna" in $workflow.skip_analysis\n+ --skip-tmrna\n+ #end if\n+ #if "skip_rrna" in $workflow.skip_analysis\n+ --skip-rrna\n+ #end if\n+ #if "skip_ncrna" in $workflow.skip_analysis\n+ --skip-ncrna\n+ #end if\n+ #if "skip_ncrna_region" in $workflow.skip_analysis\n+ --skip-ncrna-region\n+ #end if\n+ #if "skip_crispr" in $workflow.skip_analysis\n+ --skip-crispr\n+ #end if\n+ #if "skip_cds" in $workflow.skip_analysis\n+ --skip-cds\n+ #end if\n+ #if "skip_sorf" in $workflow.skip_analysis\n+ --skip-sorf\n+ #end if\n+ #if "skip_gap" in $workflow.skip_analysis\n+ --skip-gap\n+ #end if\n+ #if "skip_ori" in $workflow.skip_analysis\n+ --skip-ori\n+ #end if\n+\n+ #*======================================\n+ Genome file\n+ ======================================*#\n+ \'$input_option.input_file\'\n+ #*======================================\n+ LOG file\n+ ======================================*#\n+ | tee \'$logfile\'\n+ ]]></command>\n+ <inputs>\n+ <!-- DB and fil'..b'losely related but distinct protein families.\n+ This is achieved via an alignment-free sequence identification (AFSI) approach\n+ using full-length MD5 protein sequence hash digests.\n+ *Small proteins/short open reading frames*\n+ Bakta detects and annotates small proteins/short open reading frames (sORF).\n+\n+ *Expert annotation systems*\n+ To provide high quality annotations for certain proteins of higher interest, e.g. AMR & VF genes,\n+ Bakta includes & merges different expert annotation systems.\n+ Currently, Bakta uses NCBI\'s AMRFinderPlus for AMR gene annotations\n+ as well as an generalized protein sequence expert system with distinct\n+ coverage, identity and priority values for each sequence, currenlty comprising the VFDB as well as NCBI\'s BlastRules.\n+\n+ *Comprehensive workflow*\n+ Bakta annotates ncRNA cis-regulatory regions, oriC/oriV/oriT\n+ and assembly gaps as well as standard feature types: tRNA, tmRNA, rRNA, ncRNA genes, CRISPR, CDS.\n+\n+ *GFF3 & INSDC conform annotations*\n+ Bakta writes GFF3 and INSDC-compliant (Genbank & EMBL) annotation files ready for submission\n+ (checked via GenomeTools GFF3Validator, table2asn_GFF and ENA Webin-CLI for GFF3 and EMBL file formats,\n+ respectively for representative genomes of all ESKAPE species).\n+\n+ *Bacteria & plasmids*\n+ Bakta was designed to annotate bacteria (isolates & MAGs) and plasmids, only.\n+\n+ **Input options**\n+ 1. Choose a genome or assembly in fasta format to use bakta annotations\n+ 2. Choose A version of the Bakta database\n+\n+ **Organism options**\n+ You can specify informations about analysed fasta as text input for:\n+ - genus\n+ - species\n+ - strain\n+ - plasmid\n+\n+ **Annotation options**\n+ 1. You can specify if all sequences (chromosome or plasmids) are complete or not\n+ 2. You can add your own prodigal traingin file for CDS prediction\xc5\x93\n+ 3. The translation table could be modified, default is the 11th for bacteria\n+ 4. You can specify if bacteria is gram -/+ or unknonw (default value unknow)\n+ 5. You can keep the name of contig present in the input file\n+ 6. You can specify your own replicon table as a TSV/CSV file\n+ 7. The compliance option is for ready to submit annotation file to Public database\n+ as ENA, Genbank EMBL\n+ 8. You can specify a protein sequence file for annotation in GenBank or fasta formats\n+ Using the Fasta format, each reference sequence can be provided in a short or long format:\n+\n+ # short:\n+ >id gene~~~product~~~dbxrefs\n+ MAQ...\n+\n+ # long:\n+ >id min_identity~~~min_query_cov~~~min_subject_cov~~~gene~~~product~~~dbxrefs\n+ MAQ...\n+\n+ **Skip steps**\n+ Some steps could be skiped:\n+ - skip-trna Skip tRNA detection & annotation\n+ - skip-tmrna Skip tmRNA detection & annotation\n+ - skip-rrna Skip rRNA detection & annotation\n+ - skip-ncrna Skip ncRNA detection & annotation\n+ - skip-ncrna-region Skip ncRNA region detection & annotation\n+ - skip-crispr Skip CRISPR array detection & annotation\n+ - skip-cds Skip CDS detection & annotation\n+ - skip-pseudo Skip pseudogene detection & annotation\n+ - skip-sorf Skip sORF detection & annotation\n+ - skip-gap Skip gap detection & annotation\n+ - skip-ori Skip oriC/oriT detection & annotation\n+\n+ **Output options**\n+ Bakta produce numbers of output files, you can select what type of file you want:\n+ - Summary of the annotation\n+ - Annotated files\n+ - Sequence files for nucleotide and/or amino acid\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 1a27ad3d0cdf macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,28 @@ +<macros> + <token name="@TOOL_VERSION@">1.4.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="version_command"> + <version_command><![CDATA[bakta --version]]></version_command> + </xml> + <xml name="edam"> + <edam_topics> + <edam_topic>topic_3174</edam_topic> + </edam_topics> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type='bio.tools'>Bakta</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bakta</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1099/mgen.0.000685</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/NC_002127.1.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_002127.1.fna Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,20 @@ +>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 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,87 @@ +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, 13:06:54 +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 +// |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.ffn Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.fna Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>contig_1 [completeness=complete] [topology=circular] [gcode=11] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,83 @@ +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, 13:06:54 + 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 +// |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,36 @@ +##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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.hypotheticals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,90 @@ +{ + "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 13:06:53", + "end": "2022-08-22 13:06:54" + }, + "version": { + "bakta": "1.4.2", + "db": "3.0" + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,90 @@ +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/tmpb092rhfs/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 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/TEST_1/TEST_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/TEST_1.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,89 @@ +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, 13:07:08 +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 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.ffn Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.fna Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,24 @@ +>NC_002127.1 Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,85 @@ +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, 13:07:08 + 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 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,37 @@ +##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 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.hypotheticals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,89 @@ +{ + "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 13:07:07", + "end": "2022-08-22 13:07:08" + }, + "version": { + "bakta": "1.4.2", + "db": "3.0" + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,88 @@ +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/tmpb092rhfs/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 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/TEST_2/TEST_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_2/TEST_2.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/TEST_3/TEST_3.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,62 @@ +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, 13:07:22 +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 000000000000 -r 1a27ad3d0cdf test-data/TEST_3/TEST_3.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.fna Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>contig_1 [completeness=complete] [topology=circular] [gcode=11] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_3/TEST_3.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,58 @@ +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, 13:07:22 + 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 000000000000 -r 1a27ad3d0cdf test-data/TEST_3/TEST_3.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,34 @@ +##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 000000000000 -r 1a27ad3d0cdf test-data/TEST_3/TEST_3.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,42 @@ +{ + "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 13:07:21", + "end": "2022-08-22 13:07:22" + }, + "version": { + "bakta": "1.4.2", + "db": "3.0" + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_3/TEST_3.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,55 @@ +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/tmpb092rhfs/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 000000000000 -r 1a27ad3d0cdf test-data/TEST_3/TEST_3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_3/TEST_3.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,87 @@ +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, 13:08:00 +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 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.ffn Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.fna Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>p2 [completeness=complete] [topology=circular] [gcode=4] [plasmid-name=pOSAK1] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,83 @@ +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, 13:08:00 + 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 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,13 @@ +##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 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.hypotheticals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,89 @@ +{ + "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 13:07:59", + "end": "2022-08-22 13:08:00" + }, + "version": { + "bakta": "1.4.2", + "db": "3.0" + } +} \ No newline at end of file |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,91 @@ +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/tmpb092rhfs/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 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.tsv Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/TEST_4/TEST_4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_4/TEST_4.txt Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/TEST_5/TEST_5.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_5/TEST_5.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,55 @@ +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/tmpb092rhfs/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 000000000000 -r 1a27ad3d0cdf test-data/TEST_5/TEST_5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_5/TEST_5.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/prodigal.tf |
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| Binary file test-data/prodigal.tf has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/replicons.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replicons.tsv Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,3 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m |
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| Binary file test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#taxgroup protein_accession protein_gi +Escherichia AAA21095.1 151858 |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pin |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,1 @@ +3.10.16 |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/fam.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amrfinderplus-db/2021-09-30.1/fam.tab Thu Sep 01 17:28:43 2022 +0000 |
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| b'@@ -0,0 +1,1744 @@\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 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,2 @@ +#taxgroup gpipe_taxgroup number_of_nucl_ref_genes +Acinetobacter_baumannii Acinetobacter 0 |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/amrfinderplus-db/2021-09-30.1/version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/amrfinderplus-db/2021-09-30.1/version.txt Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,1 @@ +2021-09-30.1 |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/antifam.h3f |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/ncRNA-regions.i1f |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/ncRNA-regions.i1p |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/oric.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/oric.fna Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,4 @@ +>ORI10010001 +TATTCTTCTATAACATTGTCAAGAATGATAGTTAAAATTCTCGAAATTGGGATATTAACTGCTTTGGAGTAATTTCTAACTTTTTGTCATACTCTTTGACTTGTATAGAAGTGTACACCTGTATCTAGTTTTTCTTGGCGTTCAACAGGAACTATTCCTGGTATTTTTGTTTTAGGTTGGGGAGGAATAGGCTGTGGTTGTGTGAATTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATGATATTGAAAATTTTGTTCCTCTTGAAAATATCTCTCTTTTTTTGGTTTTCCAGAAAAATTTGATGAAAAAGATTTTTCTTCATTTCAATTTTCAAGATTATTTTCATTTTGTTGATTTATTTGCTCAGGCTGTTGAAATGAATTATTTTTTGATCAAAAAGATTTTGGAAAGGTTTTTTCAAAAGCAGATAAAGGTCCAAAATCAAATGAAGATGAATCTTTGTCAAAAGATGTTTCTTCTCTTTTTGACAAATTTTGTTTTTGATTAAACTTATTTTTATTTTGGGGTGTTACTTTTTCTTTTATGGAAAACAAATCTTCTTCTAAAAGACTTTGTTCTGGGTCATCATCTTGTGCTAAATCAAAGAAAAAACGTTTCTTTTTGTTA +>ORI10010003 +GGCGTAGACACTGAATTCGATGGGGATAAGTGGTGGATAAAAGAATATAAATTAGTCATTACACTTTACTCACGAATATCCCCCTTTTTTTAGAGAAAAAATATACTTTCTTCACAAGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCGAGACATAAGCACTTATCCAGATATTCACAGTTACTATTATGTGATACGACTACATTCTTTATACTTATAAGATTAATAAGGAGGAAACTAACT |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/orit.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/orit.fna Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,4 @@ +>CP019995|MOBP +GTAGAATCGTTTAGTATGAGAATAGAAAACCAACGGTTTTCATGAACTTACTAAACGATTCTAC +>CP012386|MOBP +AGAACAATCAACAACTAATTAGGCAAATTAAGGGGTGCTAAACAACTGCTAGTAGGTGCTAGAGATGTGCTATAAAGGGTGCTAGTTTGGTGCTAGTTACTGCTAAATACGTGCTAGTTTAGGTGCTAGAAACGTGCTATATGGTGCTAAAAAGGTGCTAGTTTGCATGAAGTTACCTGCTAGCCAAGTGCTAGTGGCGTTCGTTTTTGGGTCCCACGGGAAAGCCTTGCACTGCAAGGCGGGTCAGCTTGTCTGACCCCCATTTCCCCTTATGCTCTTCCGAAACACAAAGCGCAATTAAGCGAATACTAGAGAATAAATA |
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| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/rRNA.i1p |
| b |
| Binary file test-data/test-db/rRNA.i1p has changed |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/rfam-go.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/rfam-go.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Rfam:RF00001 GO:0003735 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/sorf.dmnd |
| b |
| Binary file test-data/test-db/sorf.dmnd has changed |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test-db/version.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/version.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,53 @@ +{ + "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" + } + ] +} |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/test_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_database.loc Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +# 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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/NC_002127.1.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/NC_002127.1.fna Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,20 @@ +>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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,87 @@ +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 +// |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.ffn Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.fna Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>contig_1 [completeness=complete] [topology=circular] [gcode=11] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,83 @@ +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 +// |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,36 @@ +##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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.hypotheticals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,90 @@ +{ + "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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,90 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_1/TEST_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_1/TEST_1.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,89 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.ffn Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.fna Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,24 @@ +>NC_002127.1 Escherichia coli O157:H7 str. Sakai plasmid pOSAK1, complete sequence +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,85 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,37 @@ +##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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.hypotheticals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,89 @@ +{ + "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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,88 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_2/TEST_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_2/TEST_2.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,62 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.fna Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>contig_1 [completeness=complete] [topology=circular] [gcode=11] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,58 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,34 @@ +##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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,42 @@ +{ + "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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,55 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_3/TEST_3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_3/TEST_3.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.embl Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,87 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.ffn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.ffn Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +ATGACAAAACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGAAGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTTACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGAAGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGACAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAGGCTTATGGCAGATTAG +>IHHALP_00010 hypothetical protein +ATGAACAAGCAGCAGCAAACTGCACTCAACATGGCGGGATTCATAAAAAGCCAGAGCCTGACGCTGCTCGAAAAACTGGACGCACTCGATGCTGACGAGCAGGCCACCATGTGTGAGAAGCTGCACGAACTCGCAGAAGAACAAATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTACTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTGAAGAAAAAGAAAAGCAAGGGTGATGTTTTTTTTGATTTAATAATTCCTAACGGTGGAAAAAAAGATCGTTACGTCTATACGTCATTTAATGGCGAGAAGTTTTCAAGTTACACATTAAACAAAGTTACGAAAACTGATGAATATAATGATTTATCTGAGCTCTCGGCTTCGTTCTTTAAAAAAAACTTTGATAAGATCAACGTAAACCTTCTATCCAAAGCCACATCATTTGCTTTGAAAAAAGGCATTCCAATATAA |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.fna Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,24 @@ +>p2 [completeness=complete] [topology=circular] [gcode=4] [plasmid-name=pOSAK1] +TTCTTCTGCGAGTTCGTGCAGCTTCTCACACATGGTGGCCTGCTCGTCAGCATCGAGTGC +GTCCAGTTTTTCGAGCAGCGTCAGGCTCTGGCTTTTTATGAATCCCGCCATGTTGAGTGC +AGTTTGCTGCTGCTTGTTCATCTTTCTGTTTTCTCCGTTCTGTCTGTCATCTGCGTCGTG +TGATTATATCGCGCACCACTTTTCGACCGTCTTACCGCCGGTATTCTGCCGACGGACATT +TCAGTCAGACAACACTGTCACTGCCAAAAAACAGCAGTGCTTTGTTGGTAATTCGAACTT +GCAGACAGGACAGGATGTGCAATTGTTATACCGCGCATACATGCACGCTATTACAATTAC +CCTGGTCAGGGCTTCGCCCCGACACCCCATGTCAGATACGGAGCCATGTTTTATGACAAA +ACGAAGTGGAAGTAATACGCGCAGGCGGGCTATCAGTCGCCCTGTTCGTCTGACGGCAGA +AGAAGACCAGGAAATCAGAAAAAGGGCTGCTGAATGCGGCAAGACCGTTTCTGGTTTTTT +ACGGGCGGCAGCTCTCGGTAAGAAAGTTAACTCACTGACTGATGACCGGGTGCTGAAAGA +AGTTATGCGACTGGGGGCGTTGCAGAAAAAACTCTTTATCGACGGCAAGCGTGTCGGGGA +CAGAGAGTATGCGGAGGTGCTGATCGCTATTACGGAGTATCACCGTGCCCTGTTATCCAG +GCTTATGGCAGATTAGCTTCCCGGAGAGAAACTGTCGAAAACAGACGGTATGAACGCCGT +AAGCCCCCAAACCGATCGCCATTCACTTTCATGCATAGCTATGCAGTGAGCTGAAAGCGA +TCCTGACGCATTTTTCCGGTTTACCCCGGGGAAAACATCTCTTTTTGCGGTGTCTGCGTC +AGAATCGCGTTCAGCGCGTTTTGGCGGTGCGCGTAATGAGACGTTATGGTAAATGTCTTC +TGGCTTGATATTATATTGGAATGCCTTTTTTCAAAGCAAATGATGTGGCTTTGGATAGAA +GGTTTACGTTGATCTTATCAAAGTTTTTTTTAAAGAACGAAGCCGAGAGCTCAGATAAAT +CATTATATTCATCAGTTTTCGTAACTTTGTTTAATGTGTAACTTGAAAACTTCTCGCCAT +TAAATGACGTATAGACGTAACGATCTTTTTTTCCACCGTTAGGAATTATTAAATCAAAAA +AAACATCACCCTTGCTTTTCTTTTTCTTCAAGTCGGATTCGATTTTTGAGAAAAATTCGC +TCGGGCTATAAATATCAGTAGCATAGACAATAAATAAAGTTTTATCTTTATTTTTTATTG +CTTCTATTTG |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.gbff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.gbff Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,83 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.gff3 Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,13 @@ +##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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.hypotheticals.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.hypotheticals.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>IHHALP_00005 hypothetical protein +MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD +>IHHALP_00010 hypothetical protein +MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELAEEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKGIPI |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.hypotheticals.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.hypotheticals.tsv Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,5 @@ +#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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,89 @@ +{ + "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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,91 @@ +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]. |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +#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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_4/TEST_4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_4/TEST_4.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_5/TEST_5.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_5/TEST_5.log Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,55 @@ +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]. |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/TEST_5/TEST_5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/TEST_5/TEST_5.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,29 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/prodigal.tf |
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| Binary file test-data/tmp/prodigal.tf has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/replicons.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/replicons.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +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 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3f has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3i has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3m has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR.LIB.h3p has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-mutation.tab Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-suppress Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#taxgroup protein_accession protein_gi +Escherichia AAA21095.1 151858 |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt-susceptible.tab Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#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 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pdb |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pdb has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.phr |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.phr has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pin |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pin has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.psq |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.psq has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.ptf |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.ptf has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pto |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMRProt.pto has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ndb has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nhr has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nin has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.not |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.not has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nsq |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.ntf has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto |
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| Binary file test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/AMR_CDS.nto has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/database_format_version.txt Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +3.10.16 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/fam.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/fam.tab Thu Sep 01 17:28:43 2022 +0000 |
| b |
| b'@@ -0,0 +1,1744 @@\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' |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/taxgroup.tab Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#taxgroup gpipe_taxgroup number_of_nucl_ref_genes +Acinetobacter_baumannii Acinetobacter 0 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/version.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/amrfinderplus-db/2021-09-30.1/version.txt Thu Sep 01 17:28:43 2022 +0000 |
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| @@ -0,0 +1,1 @@ +2021-09-30.1 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/antifam.h3f |
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| Binary file test-data/tmp/test-db/antifam.h3f has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/antifam.h3i |
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| Binary file test-data/tmp/test-db/antifam.h3i has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/antifam.h3m |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/antifam.h3p |
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| Binary file test-data/tmp/test-db/antifam.h3p has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/bakta.db |
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| Binary file test-data/tmp/test-db/bakta.db has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/expert-protein-sequences.dmnd |
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| Binary file test-data/tmp/test-db/expert-protein-sequences.dmnd has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-genes.i1f |
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| Binary file test-data/tmp/test-db/ncRNA-genes.i1f has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-genes.i1i |
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| Binary file test-data/tmp/test-db/ncRNA-genes.i1i has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-genes.i1m |
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| Binary file test-data/tmp/test-db/ncRNA-genes.i1m has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-genes.i1p |
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| Binary file test-data/tmp/test-db/ncRNA-genes.i1p has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-regions.i1f |
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| Binary file test-data/tmp/test-db/ncRNA-regions.i1f has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-regions.i1i |
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| Binary file test-data/tmp/test-db/ncRNA-regions.i1i has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-regions.i1m |
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| Binary file test-data/tmp/test-db/ncRNA-regions.i1m has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/ncRNA-regions.i1p |
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| Binary file test-data/tmp/test-db/ncRNA-regions.i1p has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/oric.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/oric.fna Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>ORI10010001 +TATTCTTCTATAACATTGTCAAGAATGATAGTTAAAATTCTCGAAATTGGGATATTAACTGCTTTGGAGTAATTTCTAACTTTTTGTCATACTCTTTGACTTGTATAGAAGTGTACACCTGTATCTAGTTTTTCTTGGCGTTCAACAGGAACTATTCCTGGTATTTTTGTTTTAGGTTGGGGAGGAATAGGCTGTGGTTGTGTGAATTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATGATATTGAAAATTTTGTTCCTCTTGAAAATATCTCTCTTTTTTTGGTTTTCCAGAAAAATTTGATGAAAAAGATTTTTCTTCATTTCAATTTTCAAGATTATTTTCATTTTGTTGATTTATTTGCTCAGGCTGTTGAAATGAATTATTTTTTGATCAAAAAGATTTTGGAAAGGTTTTTTCAAAAGCAGATAAAGGTCCAAAATCAAATGAAGATGAATCTTTGTCAAAAGATGTTTCTTCTCTTTTTGACAAATTTTGTTTTTGATTAAACTTATTTTTATTTTGGGGTGTTACTTTTTCTTTTATGGAAAACAAATCTTCTTCTAAAAGACTTTGTTCTGGGTCATCATCTTGTGCTAAATCAAAGAAAAAACGTTTCTTTTTGTTA +>ORI10010003 +GGCGTAGACACTGAATTCGATGGGGATAAGTGGTGGATAAAAGAATATAAATTAGTCATTACACTTTACTCACGAATATCCCCCTTTTTTTAGAGAAAAAATATACTTTCTTCACAAGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCGAGACATAAGCACTTATCCAGATATTCACAGTTACTATTATGTGATACGACTACATTCTTTATACTTATAAGATTAATAAGGAGGAAACTAACT |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/orit.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/orit.fna Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>CP019995|MOBP +GTAGAATCGTTTAGTATGAGAATAGAAAACCAACGGTTTTCATGAACTTACTAAACGATTCTAC +>CP012386|MOBP +AGAACAATCAACAACTAATTAGGCAAATTAAGGGGTGCTAAACAACTGCTAGTAGGTGCTAGAGATGTGCTATAAAGGGTGCTAGTTTGGTGCTAGTTACTGCTAAATACGTGCTAGTTTAGGTGCTAGAAACGTGCTATATGGTGCTAAAAAGGTGCTAGTTTGCATGAAGTTACCTGCTAGCCAAGTGCTAGTGGCGTTCGTTTTTGGGTCCCACGGGAAAGCCTTGCACTGCAAGGCGGGTCAGCTTGTCTGACCCCCATTTCCCCTTATGCTCTTCCGAAACACAAAGCGCAATTAAGCGAATACTAGAGAATAAATA |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/pfam.h3f |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/rRNA.i1f |
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| Binary file test-data/tmp/test-db/rRNA.i1f has changed |
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| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/rRNA.i1i |
| b |
| Binary file test-data/tmp/test-db/rRNA.i1i has changed |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/rRNA.i1m |
| b |
| Binary file test-data/tmp/test-db/rRNA.i1m has changed |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/rRNA.i1p |
| b |
| Binary file test-data/tmp/test-db/rRNA.i1p has changed |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/rfam-go.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/rfam-go.tsv Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Rfam:RF00001 GO:0003735 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/sorf.dmnd |
| b |
| Binary file test-data/tmp/test-db/sorf.dmnd has changed |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test-db/version.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test-db/version.json Thu Sep 01 17:28:43 2022 +0000 |
| [ |
| @@ -0,0 +1,53 @@ +{ + "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" + } + ] +} |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/test_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/test_database.loc Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +# 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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/tmp/user-proteins.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmp/user-proteins.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf test-data/user-proteins.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user-proteins.faa Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>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 |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf tool-data/bakta_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bakta_database.loc.sample Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +#This is a sample file distributed with Galaxy that enables tools +#file has this format (white space characters are TAB characters) +test-db-bakta "Database test" ${__HERE__}/test-db |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="bakta_database" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/bakta_database.loc.sample" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 1a27ad3d0cdf tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Sep 01 17:28:43 2022 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="bakta_database" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/test_database.loc" /> + </table> +</tables> |