Merge pull request #124 from UPHL-BioNGS/update-2023-09-20

Update 2023 09 20
UPHL-BioNGS · Sep 21, 2023 · d9b10b5 · d9b10b5
2 parents 0a5b13d + bc31654
commit d9b10b5
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Showing 193 changed files with 541 additions and 226 deletions.
diff --git a/.github/workflows/current.yml b/.github/workflows/current.yml
@@ -0,0 +1,38 @@
+name: Test Grandeur with current datasets workflow
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: Checkout LFS objects
+        run: git lfs checkout
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+          
+      - name: Run Grandeur
+        run: |
+          docker --version
+
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/863/225/GCA_904863225.1_KSB1_6J/GCA_904863225.1_KSB1_6J_genomic.fna.gz           && gzip -d GCA_904863225.1_KSB1_6J_genomic.fna.gz
+          
+          mkdir fastas
+          mv *fna fastas/.
+
+          nextflow run . -profile docker --maxcpus 2 --medcpus 2
+
+          cat grandeur/grandeur_summary.tsv
diff --git a/.github/workflows/datasets.yml b/.github/workflows/datasets.yml
diff --git a/assets/included_genomes.txt b/assets/included_genomes.txt
@@ -0,0 +1,182 @@
+Assembly_Accession	Assembly_Refseq_Category	Assembly_Level	Organism_Name	Assembly_Stats_Total_Ungapped_Length
+GCF_000816225.1		Complete_Genome	Campylobacter_lari_subsp._concheus_LMG_11760	1502102
+GCA_008011615.1		Contig	Campylobacter_upsaliensis	1647995
+GCA_008011635.1		Scaffold	Campylobacter_coli	1693591
+GCA_008011525.1		Contig	Campylobacter_jejuni_subsp._jejuni	1739221
+GCF_001643955.1		Complete_Genome	Campylobacter_hyointestinalis_subsp._hyointestinalis_LMG_9260	1753385
+GCF_000015085.1		Complete_Genome	Campylobacter_fetus_subsp._fetus_82-40	1773615
+GCF_000495505.1		Complete_Genome	Campylobacter_fetus_subsp._testudinum_03-427	1775480
+GCF_000017485.1		Complete_Genome	Campylobacter_jejuni_subsp._doylei_269.97	1845106
+GCF_000759515.1		Complete_Genome	Campylobacter_fetus_subsp._venerealis_97/608	2000424
+GCF_016724885.1		Complete_Genome	Streptococcus_dysgalactiae	2151179
+GCF_013625895.1		Scaffold	Listeria_monocytogenes	2717964
+GCF_017363645.1		Contig	Listeria_marthii	2737526
+GCF_017363655.1		Contig	Listeria_innocua	2766718
+GCF_017363615.1		Contig	Listeria_innocua	2779613
+GCF_013626145.1		Scaffold	Listeria_monocytogenes	2798903
+GCF_013625995.1		Contig	Listeria_monocytogenes	2823092
+GCF_002489005.1		Contig	Listeria_welshimeri	2824610
+GCF_014526935.1		Contig	Listeria_monocytogenes	2876424
+GCF_017363605.1		Contig	Listeria_seeligeri	2926127
+GCF_000252975.1		Complete_Genome	Listeria_ivanovii_subsp._ivanovii_PAM_55	2928879
+GCF_001466295.1		Contig	Listeria_monocytogenes	2980363
+GCF_009665395.1		Complete_Genome	Vibrio_cincinnatiensis	3799536
+GCF_009665235.1		Complete_Genome	Vibrio_metschnikovii	3875681
+GCA_003311965.1		Contig	Vibrio_paracholerae	3896089
+GCF_009665255.1		Complete_Genome	Vibrio_metoecus	3979875
+GCF_009665275.1		Complete_Genome	Vibrio_metoecus	3988124
+GCA_009665515.2		Chromosome	Vibrio_cholerae	4098703
+GCF_009665295.1		Complete_Genome	Grimontia_hollisae	4130266
+GCF_009665215.1		Complete_Genome	Vibrio_navarrensis	4308461
+GCA_007681265.1		Scaffold	Mixta_calida	4343751
+GCA_013588055.1		Complete_Genome	Salmonella_enterica_subsp._houtenae	4440304
+GCF_011605535.1		Scaffold	Cronobacter_turicensis	4466353
+GCF_009665195.1		Complete_Genome	Vibrio_mimicus	4476214
+GCA_009665415.1		Complete_Genome	Vibrio_cidicii	4632930
+GCF_015137655.1		Complete_Genome	Enterobacter_bugandensis	4635750
+GCF_000026225.1		Complete_Genome	Escherichia_fergusonii_ATCC_35469	4643861
+GCF_018597265.1		Contig	Enterobacter_dykesii	4652802
+GCA_011388235.1		Complete_Genome	Salmonella_enterica	4653561
+GCF_009665355.1		Chromosome	Vibrio_fluvialis	4654634
+GCF_000512125.1		Complete_Genome	Escherichia_albertii_KF1	4701875
+GCF_023547145.1		Complete_Genome	Providencia_stuartii	4837555
+GCF_900638065.1		Complete_Genome	Citrobacter_youngae	4867355
+GCF_002741475.1		Complete_Genome	Escherichia_coli_O27:H7	4952219
+GCF_009665335.1		Complete_Genome	Vibrio_furnissii	5000528
+GCF_009665455.1		Chromosome	Vibrio_vulnificus	5015805
+GCF_009665475.1		Complete_Genome	Vibrio_vulnificus	5079985
+GCF_023702375.1		Contig	Enterobacter_cloacae	5112849
+GCF_009665435.1		Complete_Genome	Vibrio_alginolyticus	5137878
+GCA_023650915.1		Complete_Genome	Vibrio_alginolyticus	5150420
+GCF_009665495.1		Complete_Genome	Vibrio_parahaemolyticus	5397131
+GCF_009665315.1		Complete_Genome	Vibrio_harveyi	5751647
+GCF_012986205.1		Contig	Pseudomonas_nitroreducens	6757787
+GCF_008632635.1	representative_genome	Complete_Genome	Acinetobacter_baumannii	3980230
+GCF_016576965.1	representative_genome	Complete_Genome	Acinetobacter_bereziniae	4729151
+GCF_002055515.1	representative_genome	Complete_Genome	Acinetobacter_calcoaceticus	4115994
+GCF_002370525.2	representative_genome	Complete_Genome	Acinetobacter_guillouiae	4648418
+GCF_003323815.1	representative_genome	Complete_Genome	Acinetobacter_haemolyticus	3441166
+GCF_018336855.1	representative_genome	Complete_Genome	Acinetobacter_junii	3438557
+GCF_013122135.1	representative_genome	Complete_Genome	Acinetobacter_lactucae	3973648
+GCF_005281455.1	representative_genome	Complete_Genome	Acinetobacter_nosocomialis_M2	3824973
+GCF_000191145.1	reference_genome	Complete_Genome	Acinetobacter_pittii_PHEA-2	3862530
+GCF_000367945.1	representative_genome	Scaffold	Acinetobacter_proteolyticus	4249637
+GCF_003258335.1	representative_genome	Complete_Genome	Acinetobacter_radioresistens	3089777
+GCF_010918895.1	representative_genome	Complete_Genome	Acinetobacter_schindleri	3337186
+GCF_016064815.1	representative_genome	Complete_Genome	Acinetobacter_seifertii	4070688
+GCF_018409485.1	representative_genome	Complete_Genome	Acinetobacter_variabilis	3198423
+GCF_000967305.2	representative_genome	Complete_Genome	Alcaligenes_faecalis	4248684
+GCF_009730395.1	representative_genome	Complete_Genome	Campylobacter_coli	1716536
+GCF_011600945.2	representative_genome	Complete_Genome	Campylobacter_fetus	1804582
+GCF_013372165.1	representative_genome	Complete_Genome	Campylobacter_hyointestinalis_subsp._lawsonii	1808149
+GCF_000009085.1	reference_genome	Complete_Genome	Campylobacter_jejuni_subsp._jejuni_NCTC_11168_=_ATCC_700819	1641481
+GCF_000019205.1	representative_genome	Complete_Genome	Campylobacter_lari_RM2100	1571661
+GCF_014931075.1	representative_genome	Complete_Genome	Campylobacter_peloridis	1725253
+GCF_000816305.1	representative_genome	Complete_Genome	Campylobacter_subantarcticus_LMG_24377	1852995
+GCF_916098265.1	representative_genome	Complete_Genome	Campylobacter_upsaliensis	1656401
+GCF_001558935.2	representative_genome	Complete_Genome	Citrobacter_amalonaticus	5084037
+GCF_009648935.1	representative_genome	Complete_Genome	Citrobacter_braakii	4917491
+GCF_003938205.1	representative_genome	Scaffold	Citrobacter_farmeri	5026053
+GCF_003812345.1	representative_genome	Complete_Genome	Citrobacter_freundii	5102161
+GCF_003429605.1	representative_genome	Scaffold	Citrobacter_gillenii	5165904
+GCF_000018045.1	representative_genome	Complete_Genome	Citrobacter_koseri_ATCC_BAA-895	4735357
+GCF_004801125.1	representative_genome	Scaffold	Citrobacter_murliniae	5024821
+GCF_019047765.1	representative_genome	Complete_Genome	Citrobacter_pasteurii	5021319
+GCF_008693605.1	representative_genome	Complete_Genome	Citrobacter_portucalensis	4929340
+GCF_018128425.1	representative_genome	Complete_Genome	Citrobacter_sedlakii	4967243
+GCF_008693645.1	representative_genome	Complete_Genome	Citrobacter_werkmanii	5049303
+GCF_000063585.1	representative_genome	Complete_Genome	Clostridium_botulinum_A_str._ATCC_3502	3903260
+GCF_020138775.1	representative_genome	Complete_Genome	Clostridium_perfringens	3275424
+GCF_020450145.1	representative_genome	Chromosome	Clostridium_sporogenes	4246023
+GCF_001277235.1	representative_genome	Complete_Genome	Cronobacter_dublinensis_subsp._dublinensis_LMG_23823	4628405
+GCF_001277215.2	representative_genome	Complete_Genome	Cronobacter_malonaticus_LMG_23826	4473761
+GCF_001277195.1	representative_genome	Complete_Genome	Cronobacter_muytjensii_ATCC_51329	4364114
+GCF_003516125.1	representative_genome	Complete_Genome	Cronobacter_sakazakii	4437993
+GCF_001277175.1	representative_genome	Complete_Genome	Cronobacter_universalis_NCTC_9529	4436873
+GCF_002023665.2	representative_genome	Complete_Genome	Elizabethkingia_anophelis_R26	4058311
+GCF_002022145.1	representative_genome	Complete_Genome	Elizabethkingia_meningoseptica	4004759
+GCF_007035805.1	representative_genome	Complete_Genome	Enterobacter_asburiae	4768325
+GCF_020042625.1	representative_genome	Complete_Genome	Enterobacter_bugandensis	4734039
+GCF_019665745.1	representative_genome	Chromosome	Enterobacter_cancerogenus	4719133
+GCF_001984825.2	representative_genome	Complete_Genome	Enterobacter_chengduensis	5218125
+GCF_003594915.1	representative_genome	Contig	Enterobacter_chuandaensis	4634324
+GCF_905331265.2	representative_genome	Complete_Genome	Enterobacter_cloacae	5023439
+GCF_019048625.1	representative_genome	Complete_Genome	Enterobacter_hormaechei	4762440
+GCF_003594935.2	representative_genome	Complete_Genome	Enterobacter_huaxiensis	5037746
+GCF_000534275.1	representative_genome	Scaffold	Enterobacter_kobei	4769038
+GCF_001750725.1	representative_genome	Complete_Genome	Enterobacter_ludwigii	4952770
+GCF_022014715.1	representative_genome	Complete_Genome	Enterobacter_mori	4844012
+GCF_009176645.1	representative_genome	Complete_Genome	Enterobacter_oligotrophicus	4476585
+GCF_004331385.1	representative_genome	Contig	Enterobacter_quasihormaechei	4556005
+GCF_018597345.1	representative_genome	Contig	Enterobacter_quasimori	4639953
+GCF_003964805.1	representative_genome	Contig	Enterobacter_quasiroggenkampii	4788302
+GCF_001729805.1	representative_genome	Complete_Genome	Enterobacter_roggenkampii	4899997
+GCF_009036245.1	representative_genome	Complete_Genome	Enterobacter_sichuanensis	4711389
+GCF_000224675.1	representative_genome	Complete_Genome	Enterobacter_soli	5012132
+GCF_008364555.1	representative_genome	Scaffold	Enterobacter_vonholyi	4589407
+GCF_004331265.1	representative_genome	Contig	Enterobacter_wuhouensis	4897369
+GCF_000393015.1	representative_genome	Scaffold	Enterococcus_faecalis_EnGen0336	2862665
+GCF_009734005.1	representative_genome	Complete_Genome	Enterococcus_faecium	2919198
+GCF_016904755.1	representative_genome	Complete_Genome	Escherichia_albertii	4631903
+GCF_000008865.2	reference_genome	Complete_Genome	Escherichia_coli_O157:H7_str._Sakai	5594605
+GCF_000005845.2	reference_genome	Complete_Genome	Escherichia_coli_str._K-12_substr._MG1655	4641652
+GCF_020097475.1	representative_genome	Complete_Genome	Escherichia_fergusonii	4645928
+GCF_900475885.1	representative_genome	Complete_Genome	Haemophilus_aegyptius	1993258
+GCF_900477945.1	representative_genome	Complete_Genome	Haemophilus_haemolyticus	1934644
+GCF_000931575.1	representative_genome	Complete_Genome	Haemophilus_influenzae	1846259
+GCF_000191405.1	representative_genome	Scaffold	Haemophilus_parainfluenzae_ATCC_33392	2110314
+GCF_007632255.1	representative_genome	Complete_Genome	Klebsiella_aerogenes	5249267
+GCF_015139575.1	representative_genome	Complete_Genome	Klebsiella_michiganensis	6041841
+GCF_003812925.1	representative_genome	Complete_Genome	Klebsiella_oxytoca	5879076
+GCF_018139045.1	representative_genome	Complete_Genome	Klebsiella_pasteurii	5910952
+GCF_000240185.1	reference_genome	Complete_Genome	Klebsiella_pneumoniae_subsp._pneumoniae_HS11286	5682322
+GCF_016415705.1	representative_genome	Complete_Genome	Klebsiella_quasipneumoniae	5391123
+GCF_009648975.1	representative_genome	Complete_Genome	Klebsiella_variicola	5536651
+GCF_023195735.1	representative_genome	Complete_Genome	Kluyvera_ascorbata	5062542
+GCF_001518835.1	representative_genome	Complete_Genome	Leclercia_adecarboxylata	4803917
+GCF_001753085.1	representative_genome	Complete_Genome	Legionella_pneumophila	3504074
+GCF_019355955.1	representative_genome	Chromosome	Lelliottia_amnigena	4599009
+GCF_009648575.1	representative_genome	Complete_Genome	Listeria_innocua	2922148
+GCF_000196035.1	reference_genome	Complete_Genome	Listeria_monocytogenes_EGD-e	2944528
+GCF_902387845.1	representative_genome	Complete_Genome	Morganella_morganii	3906921
+GCF_013030075.1	representative_genome	Complete_Genome	Neisseria_gonorrhoeae	2171755
+GCF_000233595.1	representative_genome	Complete_Genome	Pantoea_ananatis_PA13	4867131
+GCF_009665375.1	representative_genome	Chromosome	Photobacterium_damselae	4426903
+GCF_003019925.1	representative_genome	Complete_Genome	Pluralibacter_gergoviae	5408082
+GCF_004116975.1	representative_genome	Complete_Genome	Proteus_hauseri	3930735
+GCF_000069965.1	representative_genome	Complete_Genome	Proteus_mirabilis_HI4320	4099895
+GCF_000754995.1	representative_genome	Scaffold	Proteus_vulgaris	3972483
+GCF_002843235.3	representative_genome	Complete_Genome	Providencia_huaxiensis	4800413
+GCF_003204135.1	representative_genome	Complete_Genome	Providencia_rettgeri	4454136
+GCF_029277985.1	representative_genome	Complete_Genome	Providencia_stuartii	4622190
+GCF_902164725.1	representative_genome	Chromosome	Pseudescherichia_vulneris	3773660
+GCF_000006765.1	reference_genome	Complete_Genome	Pseudomonas_aeruginosa_PAO1	6264404
+GCF_001597285.1	representative_genome	Complete_Genome	Pseudomonas_alcaligenes	4406305
+GCF_900215245.1	representative_genome	Chromosome	Pseudomonas_fluorescens	6511447
+GCF_001186195.1	representative_genome	Contig	Pseudomonas_fulva	5119844
+GCF_002355475.1	representative_genome	Complete_Genome	Pseudomonas_furukawaii	6242949
+GCF_012971725.1	representative_genome	Complete_Genome	Pseudomonas_multiresinivorans	6517592
+GCF_011397855.1	representative_genome	Complete_Genome	Pseudomonas_otitidis	6089454
+GCF_000412675.1	representative_genome	Complete_Genome	Pseudomonas_putida_NBRC_14164	6156701
+GCF_902374465.1	representative_genome	Scaffold	Ralstonia_pickettii	5243971
+GCF_901421005.1	representative_genome	Contig	Raoultella_ornithinolytica	5606861
+GCF_022637595.1	representative_genome	Complete_Genome	Raoultella_planticola	5646881
+GCF_000439255.1	representative_genome	Complete_Genome	Salmonella_bongori_N268-08	4773537
+GCF_000006945.2	reference_genome	Complete_Genome	Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2	4951383
+GCF_003516165.1	representative_genome	Chromosome	Serratia_marcescens	5238337
+GCF_004768745.1	representative_genome	Complete_Genome	Serratia_nematodiphila	5256558
+GCF_002290485.1	representative_genome	Contig	Shigella_boydii	4825405
+GCF_022354085.1	representative_genome	Complete_Genome	Shigella_dysenteriae	5192674
+GCF_000006925.2	reference_genome	Complete_Genome	Shigella_flexneri_2a_str._301	4828820
+GCF_013374815.1	representative_genome	Complete_Genome	Shigella_sonnei	4762774
+GCF_000013425.1	reference_genome	Complete_Genome	Staphylococcus_aureus_subsp._aureus_NCTC_8325	2821361
+GCF_900475405.1	representative_genome	Complete_Genome	Stenotrophomonas_maltophilia	4481118
+GCF_001412635.1	representative_genome	Complete_Genome	Streptococcus_anginosus	1924513
+GCF_002076835.1	representative_genome	Chromosome	Streptococcus_pneumoniae	2117267
+GCF_000221985.1	representative_genome	Complete_Genome	Streptococcus_pseudopneumoniae_IS7493	2195458
+GCF_900475035.1	representative_genome	Complete_Genome	Streptococcus_pyogenes	1746380
+GCF_008369605.1	representative_genome	Complete_Genome	Vibrio_cholerae	4138412
+GCF_000176375.1	representative_genome	Contig	Vibrio_mimicus_MB451	4313453
+GCF_012275065.1	representative_genome	Chromosome	Vibrio_navarrensis	4287126
+GCF_000196095.1	representative_genome	Complete_Genome	Vibrio_parahaemolyticus_RIMD_2210633	5165770
+GCF_002204915.1	representative_genome	Complete_Genome	Vibrio_vulnificus	5117890
diff --git a/db/Acinetobacter_baumannii_GCF_008632635.1.fna.gz b/db/Acinetobacter_baumannii_GCF_008632635.1.fna.gz
diff --git a/db/Acinetobacter_bereziniae_GCF_016576965.1.fna.gz b/db/Acinetobacter_bereziniae_GCF_016576965.1.fna.gz
diff --git a/db/Acinetobacter_calcoaceticus_GCF_002055515.1.fna.gz b/db/Acinetobacter_calcoaceticus_GCF_002055515.1.fna.gz
diff --git a/db/Acinetobacter_guillouiae_GCF_002370525.2.fna.gz b/db/Acinetobacter_guillouiae_GCF_002370525.2.fna.gz
diff --git a/db/Acinetobacter_haemolyticus_GCF_003323815.1.fna.gz b/db/Acinetobacter_haemolyticus_GCF_003323815.1.fna.gz
diff --git a/db/Acinetobacter_junii_GCF_018336855.1.fna.gz b/db/Acinetobacter_junii_GCF_018336855.1.fna.gz
diff --git a/db/Acinetobacter_lactucae_GCF_013122135.1.fna.gz b/db/Acinetobacter_lactucae_GCF_013122135.1.fna.gz
diff --git a/db/Acinetobacter_nosocomialis_M2_GCF_005281455.1.fna.gz b/db/Acinetobacter_nosocomialis_M2_GCF_005281455.1.fna.gz
diff --git a/db/Acinetobacter_pittii_PHEA-2_GCF_000191145.1.fna.gz b/db/Acinetobacter_pittii_PHEA-2_GCF_000191145.1.fna.gz
diff --git a/db/Acinetobacter_proteolyticus_GCF_000367945.1.fna.gz b/db/Acinetobacter_proteolyticus_GCF_000367945.1.fna.gz
diff --git a/db/Acinetobacter_radioresistens_GCF_003258335.1.fna.gz b/db/Acinetobacter_radioresistens_GCF_003258335.1.fna.gz
diff --git a/db/Acinetobacter_schindleri_GCF_010918895.1.fna.gz b/db/Acinetobacter_schindleri_GCF_010918895.1.fna.gz
diff --git a/db/Acinetobacter_seifertii_GCF_016064815.1.fna.gz b/db/Acinetobacter_seifertii_GCF_016064815.1.fna.gz
diff --git a/db/Acinetobacter_variabilis_GCF_018409485.1.fna.gz b/db/Acinetobacter_variabilis_GCF_018409485.1.fna.gz
diff --git a/db/Alcaligenes_faecalis_GCF_000967305.2.fna.gz b/db/Alcaligenes_faecalis_GCF_000967305.2.fna.gz
diff --git a/db/Campylobacter_coli_GCA_008011635.1.fna.gz b/db/Campylobacter_coli_GCA_008011635.1.fna.gz
diff --git a/db/Campylobacter_coli_GCF_009730395.1.fna.gz b/db/Campylobacter_coli_GCF_009730395.1.fna.gz
diff --git a/db/Campylobacter_fetus_GCF_011600945.2.fna.gz b/db/Campylobacter_fetus_GCF_011600945.2.fna.gz
diff --git a/db/Campylobacter_fetus_subsp._fetus_82-40_GCF_000015085.1.fna.gz b/db/Campylobacter_fetus_subsp._fetus_82-40_GCF_000015085.1.fna.gz
diff --git a/db/Campylobacter_fetus_subsp._testudinum_03-427_GCF_000495505.1.fna.gz b/db/Campylobacter_fetus_subsp._testudinum_03-427_GCF_000495505.1.fna.gz
diff --git a/db/Campylobacter_fetus_subsp._venerealis_GCF_000759515.1.fna.gz b/db/Campylobacter_fetus_subsp._venerealis_GCF_000759515.1.fna.gz
diff --git a/db/Campylobacter_hyointestinalis_subsp._hyointestinalis_LMG_9260_GCF_001643955.1.fna.gz b/db/Campylobacter_hyointestinalis_subsp._hyointestinalis_LMG_9260_GCF_001643955.1.fna.gz
diff --git a/db/Campylobacter_hyointestinalis_subsp._lawsonii_GCF_013372165.1.fna.gz b/db/Campylobacter_hyointestinalis_subsp._lawsonii_GCF_013372165.1.fna.gz
diff --git a/db/Campylobacter_jejuni_subsp._doylei_269.97_GCF_000017485.1.fna.gz b/db/Campylobacter_jejuni_subsp._doylei_269.97_GCF_000017485.1.fna.gz
diff --git a/db/Campylobacter_jejuni_subsp._jejuni_GCA_008011525.1.fna.gz b/db/Campylobacter_jejuni_subsp._jejuni_GCA_008011525.1.fna.gz
diff --git a/db/Campylobacter_jejuni_subsp._jejuni_NCTC_11168_ATCC_700819_GCF_000009085.1.fna.gz b/db/Campylobacter_jejuni_subsp._jejuni_NCTC_11168_ATCC_700819_GCF_000009085.1.fna.gz
diff --git a/db/Campylobacter_lari_RM2100_GCF_000019205.1.fna.gz b/db/Campylobacter_lari_RM2100_GCF_000019205.1.fna.gz
diff --git a/db/Campylobacter_lari_subsp._concheus_LMG_11760_GCF_000816225.1.fna.gz b/db/Campylobacter_lari_subsp._concheus_LMG_11760_GCF_000816225.1.fna.gz
diff --git a/db/Campylobacter_peloridis_GCF_014931075.1.fna.gz b/db/Campylobacter_peloridis_GCF_014931075.1.fna.gz
diff --git a/db/Campylobacter_subantarcticus_LMG_24377_GCF_000816305.1.fna.gz b/db/Campylobacter_subantarcticus_LMG_24377_GCF_000816305.1.fna.gz
diff --git a/db/Campylobacter_upsaliensis_GCA_008011615.1.fna.gz b/db/Campylobacter_upsaliensis_GCA_008011615.1.fna.gz
diff --git a/db/Campylobacter_upsaliensis_GCF_916098265.1.fna.gz b/db/Campylobacter_upsaliensis_GCF_916098265.1.fna.gz
diff --git a/db/Citrobacter_amalonaticus_GCF_001558935.2.fna.gz b/db/Citrobacter_amalonaticus_GCF_001558935.2.fna.gz
diff --git a/db/Citrobacter_braakii_GCF_009648935.1.fna.gz b/db/Citrobacter_braakii_GCF_009648935.1.fna.gz
diff --git a/db/Citrobacter_farmeri_GCF_003938205.1.fna.gz b/db/Citrobacter_farmeri_GCF_003938205.1.fna.gz
diff --git a/db/Citrobacter_freundii_GCF_003812345.1.fna.gz b/db/Citrobacter_freundii_GCF_003812345.1.fna.gz
diff --git a/db/Citrobacter_gillenii_GCF_003429605.1.fna.gz b/db/Citrobacter_gillenii_GCF_003429605.1.fna.gz
diff --git a/db/Citrobacter_koseri_ATCC_BAA-895_GCF_000018045.1.fna.gz b/db/Citrobacter_koseri_ATCC_BAA-895_GCF_000018045.1.fna.gz
diff --git a/db/Citrobacter_murliniae_GCF_004801125.1.fna.gz b/db/Citrobacter_murliniae_GCF_004801125.1.fna.gz
diff --git a/db/Citrobacter_pasteurii_GCF_019047765.1.fna.gz b/db/Citrobacter_pasteurii_GCF_019047765.1.fna.gz
diff --git a/db/Citrobacter_portucalensis_GCF_008693605.1.fna.gz b/db/Citrobacter_portucalensis_GCF_008693605.1.fna.gz
diff --git a/db/Citrobacter_sedlakii_GCF_018128425.1.fna.gz b/db/Citrobacter_sedlakii_GCF_018128425.1.fna.gz
diff --git a/db/Citrobacter_werkmanii_GCF_008693645.1.fna.gz b/db/Citrobacter_werkmanii_GCF_008693645.1.fna.gz
diff --git a/db/Citrobacter_youngae_GCF_900638065.1.fna.gz b/db/Citrobacter_youngae_GCF_900638065.1.fna.gz
diff --git a/db/Clostridium_botulinum_A_str._ATCC_3502_GCF_000063585.1.fna.gz b/db/Clostridium_botulinum_A_str._ATCC_3502_GCF_000063585.1.fna.gz
diff --git a/db/Clostridium_perfringens_GCF_020138775.1.fna.gz b/db/Clostridium_perfringens_GCF_020138775.1.fna.gz
diff --git a/db/Clostridium_sporogenes_GCF_020450145.1.fna.gz b/db/Clostridium_sporogenes_GCF_020450145.1.fna.gz
diff --git a/db/Cronobacter_dublinensis_subsp._dublinensis_LMG_23823_GCF_001277235.1.fna.gz b/db/Cronobacter_dublinensis_subsp._dublinensis_LMG_23823_GCF_001277235.1.fna.gz
diff --git a/db/Cronobacter_malonaticus_LMG_23826_GCF_001277215.2.fna.gz b/db/Cronobacter_malonaticus_LMG_23826_GCF_001277215.2.fna.gz
diff --git a/db/Cronobacter_muytjensii_ATCC_51329_GCF_001277195.1.fna.gz b/db/Cronobacter_muytjensii_ATCC_51329_GCF_001277195.1.fna.gz
diff --git a/db/Cronobacter_sakazakii_GCF_003516125.1.fna.gz b/db/Cronobacter_sakazakii_GCF_003516125.1.fna.gz
diff --git a/db/Cronobacter_turicensis_GCF_011605535.1.fna.gz b/db/Cronobacter_turicensis_GCF_011605535.1.fna.gz
diff --git a/db/Cronobacter_universalis_NCTC_9529_GCF_001277175.1.fna.gz b/db/Cronobacter_universalis_NCTC_9529_GCF_001277175.1.fna.gz
diff --git a/db/Elizabethkingia_anophelis_R26_GCF_002023665.2.fna.gz b/db/Elizabethkingia_anophelis_R26_GCF_002023665.2.fna.gz
diff --git a/db/Elizabethkingia_meningoseptica_GCF_002022145.1.fna.gz b/db/Elizabethkingia_meningoseptica_GCF_002022145.1.fna.gz
diff --git a/db/Enterobacter_asburiae_GCF_007035805.1.fna.gz b/db/Enterobacter_asburiae_GCF_007035805.1.fna.gz
diff --git a/db/Enterobacter_bugandensis_GCF_015137655.1.fna.gz b/db/Enterobacter_bugandensis_GCF_015137655.1.fna.gz
diff --git a/db/Enterobacter_bugandensis_GCF_020042625.1.fna.gz b/db/Enterobacter_bugandensis_GCF_020042625.1.fna.gz
diff --git a/db/Enterobacter_cancerogenus_GCF_019665745.1.fna.gz b/db/Enterobacter_cancerogenus_GCF_019665745.1.fna.gz
diff --git a/db/Enterobacter_chengduensis_GCF_001984825.2.fna.gz b/db/Enterobacter_chengduensis_GCF_001984825.2.fna.gz
diff --git a/db/Enterobacter_chuandaensis_GCF_003594915.1.fna.gz b/db/Enterobacter_chuandaensis_GCF_003594915.1.fna.gz
diff --git a/db/Enterobacter_cloacae_GCF_023702375.1.fna.gz b/db/Enterobacter_cloacae_GCF_023702375.1.fna.gz
diff --git a/db/Enterobacter_cloacae_GCF_905331265.2.fna.gz b/db/Enterobacter_cloacae_GCF_905331265.2.fna.gz
diff --git a/db/Enterobacter_dykesii_GCF_018597265.1.fna.gz b/db/Enterobacter_dykesii_GCF_018597265.1.fna.gz
diff --git a/db/Enterobacter_hormaechei_GCF_019048625.1.fna.gz b/db/Enterobacter_hormaechei_GCF_019048625.1.fna.gz
diff --git a/db/Enterobacter_huaxiensis_GCF_003594935.2.fna.gz b/db/Enterobacter_huaxiensis_GCF_003594935.2.fna.gz
diff --git a/db/Enterobacter_kobei_GCF_000534275.1.fna.gz b/db/Enterobacter_kobei_GCF_000534275.1.fna.gz
diff --git a/db/Enterobacter_ludwigii_GCF_001750725.1.fna.gz b/db/Enterobacter_ludwigii_GCF_001750725.1.fna.gz
diff --git a/db/Enterobacter_mori_GCF_022014715.1.fna.gz b/db/Enterobacter_mori_GCF_022014715.1.fna.gz
diff --git a/db/Enterobacter_oligotrophicus_GCF_009176645.1.fna.gz b/db/Enterobacter_oligotrophicus_GCF_009176645.1.fna.gz
diff --git a/db/Enterobacter_quasihormaechei_GCF_004331385.1.fna.gz b/db/Enterobacter_quasihormaechei_GCF_004331385.1.fna.gz
diff --git a/db/Enterobacter_quasimori_GCF_018597345.1.fna.gz b/db/Enterobacter_quasimori_GCF_018597345.1.fna.gz
diff --git a/db/Enterobacter_quasiroggenkampii_GCF_003964805.1.fna.gz b/db/Enterobacter_quasiroggenkampii_GCF_003964805.1.fna.gz
diff --git a/db/Enterobacter_roggenkampii_GCF_001729805.1.fna.gz b/db/Enterobacter_roggenkampii_GCF_001729805.1.fna.gz
diff --git a/db/Enterobacter_sichuanensis_GCF_009036245.1.fna.gz b/db/Enterobacter_sichuanensis_GCF_009036245.1.fna.gz
diff --git a/db/Enterobacter_soli_GCF_000224675.1.fna.gz b/db/Enterobacter_soli_GCF_000224675.1.fna.gz
diff --git a/db/Enterobacter_vonholyi_GCF_008364555.1.fna.gz b/db/Enterobacter_vonholyi_GCF_008364555.1.fna.gz
diff --git a/db/Enterobacter_wuhouensis_GCF_004331265.1.fna.gz b/db/Enterobacter_wuhouensis_GCF_004331265.1.fna.gz
diff --git a/db/Enterococcus_faecalis_EnGen0336_GCF_000393015.1.fna.gz b/db/Enterococcus_faecalis_EnGen0336_GCF_000393015.1.fna.gz
diff --git a/db/Enterococcus_faecium_GCF_009734005.1.fna.gz b/db/Enterococcus_faecium_GCF_009734005.1.fna.gz
diff --git a/db/Escherichia_albertii_GCF_016904755.1.fna.gz b/db/Escherichia_albertii_GCF_016904755.1.fna.gz
diff --git a/db/Escherichia_albertii_KF1_GCF_000512125.1.fna.gz b/db/Escherichia_albertii_KF1_GCF_000512125.1.fna.gz
diff --git a/db/Escherichia_coli_O157:H7_str._Sakai_GCF_000008865.2.fna.gz b/db/Escherichia_coli_O157:H7_str._Sakai_GCF_000008865.2.fna.gz
diff --git a/db/Escherichia_coli_O27:H7_GCF_002741475.1.fna.gz b/db/Escherichia_coli_O27:H7_GCF_002741475.1.fna.gz
diff --git a/db/Escherichia_coli_str._K-12_substr._MG1655_GCF_000005845.2.fna.gz b/db/Escherichia_coli_str._K-12_substr._MG1655_GCF_000005845.2.fna.gz
diff --git a/db/Escherichia_fergusonii_ATCC_35469_GCF_000026225.1.fna.gz b/db/Escherichia_fergusonii_ATCC_35469_GCF_000026225.1.fna.gz
diff --git a/db/Escherichia_fergusonii_GCF_020097475.1.fna.gz b/db/Escherichia_fergusonii_GCF_020097475.1.fna.gz
diff --git a/db/Grimontia_hollisae_GCF_009665295.1.fna.gz b/db/Grimontia_hollisae_GCF_009665295.1.fna.gz
diff --git a/db/Haemophilus_aegyptius_GCF_900475885.1.fna.gz b/db/Haemophilus_aegyptius_GCF_900475885.1.fna.gz
diff --git a/db/Haemophilus_haemolyticus_GCF_900477945.1.fna.gz b/db/Haemophilus_haemolyticus_GCF_900477945.1.fna.gz
diff --git a/db/Haemophilus_influenzae_GCF_000931575.1.fna.gz b/db/Haemophilus_influenzae_GCF_000931575.1.fna.gz
diff --git a/db/Haemophilus_parainfluenzae_ATCC_33392_GCF_000191405.1.fna.gz b/db/Haemophilus_parainfluenzae_ATCC_33392_GCF_000191405.1.fna.gz
diff --git a/db/Klebsiella_aerogenes_GCF_007632255.1.fna.gz b/db/Klebsiella_aerogenes_GCF_007632255.1.fna.gz
diff --git a/db/Klebsiella_michiganensis_GCF_015139575.1.fna.gz b/db/Klebsiella_michiganensis_GCF_015139575.1.fna.gz
diff --git a/db/Klebsiella_oxytoca_GCF_003812925.1.fna.gz b/db/Klebsiella_oxytoca_GCF_003812925.1.fna.gz
diff --git a/db/Klebsiella_pasteurii_GCF_018139045.1.fna.gz b/db/Klebsiella_pasteurii_GCF_018139045.1.fna.gz
diff --git a/db/Klebsiella_pneumoniae_subsp._pneumoniae_HS11286_GCF_000240185.1.fna.gz b/db/Klebsiella_pneumoniae_subsp._pneumoniae_HS11286_GCF_000240185.1.fna.gz
diff --git a/db/Klebsiella_quasipneumoniae_GCF_016415705.1.fna.gz b/db/Klebsiella_quasipneumoniae_GCF_016415705.1.fna.gz
diff --git a/db/Klebsiella_variicola_GCF_009648975.1.fna.gz b/db/Klebsiella_variicola_GCF_009648975.1.fna.gz
diff --git a/db/Kluyvera_ascorbata_GCF_023195735.1.fna.gz b/db/Kluyvera_ascorbata_GCF_023195735.1.fna.gz
diff --git a/db/Leclercia_adecarboxylata_GCF_001518835.1.fna.gz b/db/Leclercia_adecarboxylata_GCF_001518835.1.fna.gz
diff --git a/db/Legionella_pneumophila_GCF_001753085.1.fna.gz b/db/Legionella_pneumophila_GCF_001753085.1.fna.gz
diff --git a/db/Lelliottia_amnigena_GCF_019355955.1.fna.gz b/db/Lelliottia_amnigena_GCF_019355955.1.fna.gz
diff --git a/db/Listeria_innocua_GCF_009648575.1.fna.gz b/db/Listeria_innocua_GCF_009648575.1.fna.gz
diff --git a/db/Listeria_innocua_GCF_017363615.1.fna.gz b/db/Listeria_innocua_GCF_017363615.1.fna.gz
diff --git a/db/Listeria_innocua_GCF_017363655.1.fna.gz b/db/Listeria_innocua_GCF_017363655.1.fna.gz
diff --git a/db/Listeria_ivanovii_subsp._ivanovii_PAM_55_GCF_000252975.1.fna.gz b/db/Listeria_ivanovii_subsp._ivanovii_PAM_55_GCF_000252975.1.fna.gz
diff --git a/db/Listeria_marthii_GCF_017363645.1.fna.gz b/db/Listeria_marthii_GCF_017363645.1.fna.gz
diff --git a/db/Listeria_monocytogenes_EGD-e_GCF_000196035.1.fna.gz b/db/Listeria_monocytogenes_EGD-e_GCF_000196035.1.fna.gz
diff --git a/db/Listeria_monocytogenes_GCF_001466295.1.fna.gz b/db/Listeria_monocytogenes_GCF_001466295.1.fna.gz
diff --git a/db/Listeria_monocytogenes_GCF_013625895.1.fna.gz b/db/Listeria_monocytogenes_GCF_013625895.1.fna.gz
diff --git a/db/Listeria_monocytogenes_GCF_013625995.1.fna.gz b/db/Listeria_monocytogenes_GCF_013625995.1.fna.gz
diff --git a/db/Listeria_monocytogenes_GCF_013626145.1.fna.gz b/db/Listeria_monocytogenes_GCF_013626145.1.fna.gz
diff --git a/db/Listeria_monocytogenes_GCF_014526935.1.fna.gz b/db/Listeria_monocytogenes_GCF_014526935.1.fna.gz
diff --git a/db/Listeria_seeligeri_GCF_017363605.1.fna.gz b/db/Listeria_seeligeri_GCF_017363605.1.fna.gz
diff --git a/db/Listeria_welshimeri_GCF_002489005.1.fna.gz b/db/Listeria_welshimeri_GCF_002489005.1.fna.gz
diff --git a/db/Mixta_calida_GCA_007681265.1.fna.gz b/db/Mixta_calida_GCA_007681265.1.fna.gz
diff --git a/db/Morganella_morganii_GCF_902387845.1.fna.gz b/db/Morganella_morganii_GCF_902387845.1.fna.gz
diff --git a/db/Neisseria_gonorrhoeae_GCF_013030075.1.fna.gz b/db/Neisseria_gonorrhoeae_GCF_013030075.1.fna.gz
diff --git a/db/Pantoea_ananatis_PA13_GCF_000233595.1.fna.gz b/db/Pantoea_ananatis_PA13_GCF_000233595.1.fna.gz
diff --git a/db/Photobacterium_damselae_GCF_009665375.1.fna.gz b/db/Photobacterium_damselae_GCF_009665375.1.fna.gz
diff --git a/db/Pluralibacter_gergoviae_GCF_003019925.1.fna.gz b/db/Pluralibacter_gergoviae_GCF_003019925.1.fna.gz
diff --git a/db/Proteus_hauseri_GCF_004116975.1.fna.gz b/db/Proteus_hauseri_GCF_004116975.1.fna.gz
diff --git a/db/Proteus_mirabilis_HI4320_GCF_000069965.1.fna.gz b/db/Proteus_mirabilis_HI4320_GCF_000069965.1.fna.gz
diff --git a/db/Proteus_vulgaris_GCF_000754995.1.fna.gz b/db/Proteus_vulgaris_GCF_000754995.1.fna.gz
diff --git a/db/Providencia_huaxiensis_GCF_002843235.3.fna.gz b/db/Providencia_huaxiensis_GCF_002843235.3.fna.gz
diff --git a/db/Providencia_rettgeri_GCF_003204135.1.fna.gz b/db/Providencia_rettgeri_GCF_003204135.1.fna.gz
diff --git a/db/Providencia_stuartii_GCF_023547145.1.fna.gz b/db/Providencia_stuartii_GCF_023547145.1.fna.gz
diff --git a/db/Providencia_stuartii_GCF_029277985.1.fna.gz b/db/Providencia_stuartii_GCF_029277985.1.fna.gz
diff --git a/db/Pseudescherichia_vulneris_GCF_902164725.1.fna.gz b/db/Pseudescherichia_vulneris_GCF_902164725.1.fna.gz
diff --git a/db/Pseudomonas_aeruginosa_PAO1_GCF_000006765.1.fna.gz b/db/Pseudomonas_aeruginosa_PAO1_GCF_000006765.1.fna.gz
diff --git a/db/Pseudomonas_alcaligenes_GCF_001597285.1.fna.gz b/db/Pseudomonas_alcaligenes_GCF_001597285.1.fna.gz
diff --git a/db/Pseudomonas_fluorescens_GCF_900215245.1.fna.gz b/db/Pseudomonas_fluorescens_GCF_900215245.1.fna.gz
diff --git a/db/Pseudomonas_fulva_GCF_001186195.1.fna.gz b/db/Pseudomonas_fulva_GCF_001186195.1.fna.gz
diff --git a/db/Pseudomonas_furukawaii_GCF_002355475.1.fna.gz b/db/Pseudomonas_furukawaii_GCF_002355475.1.fna.gz
diff --git a/db/Pseudomonas_multiresinivorans_GCF_012971725.1.fna.gz b/db/Pseudomonas_multiresinivorans_GCF_012971725.1.fna.gz
diff --git a/db/Pseudomonas_nitroreducens_GCF_012986205.1.fna.gz b/db/Pseudomonas_nitroreducens_GCF_012986205.1.fna.gz
diff --git a/db/Pseudomonas_otitidis_GCF_011397855.1.fna.gz b/db/Pseudomonas_otitidis_GCF_011397855.1.fna.gz
diff --git a/db/Pseudomonas_putida_NBRC_14164_GCF_000412675.1.fna.gz b/db/Pseudomonas_putida_NBRC_14164_GCF_000412675.1.fna.gz
diff --git a/db/Ralstonia_pickettii_GCF_902374465.1.fna.gz b/db/Ralstonia_pickettii_GCF_902374465.1.fna.gz
diff --git a/db/Raoultella_ornithinolytica_GCF_901421005.1.fna.gz b/db/Raoultella_ornithinolytica_GCF_901421005.1.fna.gz
diff --git a/db/Raoultella_planticola_GCF_022637595.1.fna.gz b/db/Raoultella_planticola_GCF_022637595.1.fna.gz
diff --git a/db/Salmonella_bongori_N268-08_GCF_000439255.1.fna.gz b/db/Salmonella_bongori_N268-08_GCF_000439255.1.fna.gz
diff --git a/db/Salmonella_enterica_GCA_011388235.1.fna.gz b/db/Salmonella_enterica_GCA_011388235.1.fna.gz
diff --git a/db/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2_GCF_000006945.2.fna.gz b/db/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2_GCF_000006945.2.fna.gz
diff --git a/db/Salmonella_enterica_subsp._houtenae_GCA_013588055.1.fna.gz b/db/Salmonella_enterica_subsp._houtenae_GCA_013588055.1.fna.gz
diff --git a/db/Serratia_marcescens_GCF_003516165.1.fna.gz b/db/Serratia_marcescens_GCF_003516165.1.fna.gz
diff --git a/db/Serratia_nematodiphila_GCF_004768745.1.fna.gz b/db/Serratia_nematodiphila_GCF_004768745.1.fna.gz
diff --git a/db/Shigella_boydii_GCF_002290485.1.fna.gz b/db/Shigella_boydii_GCF_002290485.1.fna.gz
diff --git a/db/Shigella_dysenteriae_GCF_022354085.1.fna.gz b/db/Shigella_dysenteriae_GCF_022354085.1.fna.gz
diff --git a/db/Shigella_flexneri_2a_str._301_GCF_000006925.2.fna.gz b/db/Shigella_flexneri_2a_str._301_GCF_000006925.2.fna.gz
diff --git a/db/Shigella_sonnei_GCF_013374815.1.fna.gz b/db/Shigella_sonnei_GCF_013374815.1.fna.gz
diff --git a/db/Staphylococcus_aureus_subsp._aureus_NCTC_8325_GCF_000013425.1.fna.gz b/db/Staphylococcus_aureus_subsp._aureus_NCTC_8325_GCF_000013425.1.fna.gz
diff --git a/db/Stenotrophomonas_maltophilia_GCF_900475405.1.fna.gz b/db/Stenotrophomonas_maltophilia_GCF_900475405.1.fna.gz
diff --git a/db/Streptococcus_anginosus_GCF_001412635.1.fna.gz b/db/Streptococcus_anginosus_GCF_001412635.1.fna.gz
diff --git a/db/Streptococcus_dysgalactiae_GCF_016724885.1.fna.gz b/db/Streptococcus_dysgalactiae_GCF_016724885.1.fna.gz
diff --git a/db/Streptococcus_pneumoniae_GCF_002076835.1.fna.gz b/db/Streptococcus_pneumoniae_GCF_002076835.1.fna.gz
diff --git a/db/Streptococcus_pseudopneumoniae_IS7493_GCF_000221985.1.fna.gz b/db/Streptococcus_pseudopneumoniae_IS7493_GCF_000221985.1.fna.gz
diff --git a/db/Streptococcus_pyogenes_GCF_900475035.1.fna.gz b/db/Streptococcus_pyogenes_GCF_900475035.1.fna.gz
diff --git a/db/Vibrio_alginolyticus_GCA_023650915.1.fna.gz b/db/Vibrio_alginolyticus_GCA_023650915.1.fna.gz
diff --git a/db/Vibrio_alginolyticus_GCF_009665435.1.fna.gz b/db/Vibrio_alginolyticus_GCF_009665435.1.fna.gz
diff --git a/db/Vibrio_cholerae_GCA_009665515.2.fna.gz b/db/Vibrio_cholerae_GCA_009665515.2.fna.gz
diff --git a/db/Vibrio_cholerae_GCF_008369605.1.fna.gz b/db/Vibrio_cholerae_GCF_008369605.1.fna.gz
diff --git a/db/Vibrio_cidicii_GCA_009665415.1.fna.gz b/db/Vibrio_cidicii_GCA_009665415.1.fna.gz
diff --git a/db/Vibrio_cincinnatiensis_GCF_009665395.1.fna.gz b/db/Vibrio_cincinnatiensis_GCF_009665395.1.fna.gz
diff --git a/db/Vibrio_fluvialis_GCF_009665355.1.fna.gz b/db/Vibrio_fluvialis_GCF_009665355.1.fna.gz
diff --git a/db/Vibrio_furnissii_GCF_009665335.1.fna.gz b/db/Vibrio_furnissii_GCF_009665335.1.fna.gz
diff --git a/db/Vibrio_harveyi_GCF_009665315.1.fna.gz b/db/Vibrio_harveyi_GCF_009665315.1.fna.gz
diff --git a/db/Vibrio_metoecus_GCF_009665255.1.fna.gz b/db/Vibrio_metoecus_GCF_009665255.1.fna.gz
diff --git a/db/Vibrio_metoecus_GCF_009665275.1.fna.gz b/db/Vibrio_metoecus_GCF_009665275.1.fna.gz
diff --git a/db/Vibrio_metschnikovii_GCF_009665235.1.fna.gz b/db/Vibrio_metschnikovii_GCF_009665235.1.fna.gz
diff --git a/db/Vibrio_mimicus_GCF_009665195.1.fna.gz b/db/Vibrio_mimicus_GCF_009665195.1.fna.gz
diff --git a/db/Vibrio_mimicus_MB451_GCF_000176375.1.fna.gz b/db/Vibrio_mimicus_MB451_GCF_000176375.1.fna.gz
diff --git a/db/Vibrio_navarrensis_GCF_009665215.1.fna.gz b/db/Vibrio_navarrensis_GCF_009665215.1.fna.gz
diff --git a/db/Vibrio_navarrensis_GCF_012275065.1.fna.gz b/db/Vibrio_navarrensis_GCF_012275065.1.fna.gz
diff --git a/db/Vibrio_paracholerae_GCA_003311965.1.fna.gz b/db/Vibrio_paracholerae_GCA_003311965.1.fna.gz
diff --git a/db/Vibrio_parahaemolyticus_GCF_009665495.1.fna.gz b/db/Vibrio_parahaemolyticus_GCF_009665495.1.fna.gz
diff --git a/db/Vibrio_parahaemolyticus_RIMD_2210633_GCF_000196095.1.fna.gz b/db/Vibrio_parahaemolyticus_RIMD_2210633_GCF_000196095.1.fna.gz
diff --git a/db/Vibrio_vulnificus_GCF_002204915.1.fna.gz b/db/Vibrio_vulnificus_GCF_002204915.1.fna.gz
diff --git a/db/Vibrio_vulnificus_GCF_009665455.1.fna.gz b/db/Vibrio_vulnificus_GCF_009665455.1.fna.gz
diff --git a/db/Vibrio_vulnificus_GCF_009665475.1.fna.gz b/db/Vibrio_vulnificus_GCF_009665475.1.fna.gz
diff --git a/db/fastani_refs.tar.gz b/db/fastani_refs.tar.gz