- Updated genbank-20250603-viral-k21.zip to create genbank-20250806-viral-k21.zip
- Updated genbank-20250603-viral-k31.zip to create genbank-20250806-viral-k31.zip
- Updated genbank-20250603-viral-k51.zip to create genbank-20250806-viral-k51.zip Genbank’s viral Database Update Report
Databases updated from 20250603 to 20250806
The list of database files:
Summary of databases
Looking only at the first k-value defined in 21, 31, 51.
Summary example for the old databases
The manifest for genbank-20250603-viral-k21.zip:
[K** loading from '/group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-collect-orig.20250603-viral.csv'
path filetype: StandaloneManifestIndex
location: /group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-collect-orig.20250603-viral.csv
is database? yes
has manifest? yes
num signatures: 230959
[K** examining manifest...
total hashes: 7831871
summary of sketches:
230959 sketches with DNA, k=21, scaled=1000, abund 7831871 total hashesSummary example for the new databases
The manifest for /group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/genbank-20250806-viral-k21.zip:
[K** loading from '/group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-collect-new.20250806-viral.csv'
path filetype: StandaloneManifestIndex
location: /group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-collect-new.20250806-viral.csv
is database? yes
has manifest? yes
num signatures: 239505
[K** examining manifest...
total hashes: 7978774
summary of sketches:
239505 sketches with DNA, k=21, scaled=1000, abund 7978774 total hashesReplicate these results:
sourmash sig summarize database.zipGenome report for the updated database
Databases were updated with the update_sourmash_databases.py script in the scripts directory.
This compared the existing database against the assembly_summary.viral.txt and assembly_summary_historical.viral.txt files.
The summary report is below.
From 230959 in '/group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-collect-orig.20250603-viral.csv':
Kept 230926 in '/group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-clean-orig.20250806-viral.csv.
Removed 33 total.
Removed 30 identifiers because of suspected suspension of the genome.
Removed 3 because of changed version.
Expand for details
From 230959 in '/group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-collect-orig.20250603-viral.csv':
Kept 230926 in '/group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-clean-orig.20250806-viral.csv.
Removed 33 total.
Removed 30 identifiers because of suspected suspension of the genome.
Removed 3 because of changed version.
---- 32 included into the bad list category ----
GCA_000885255.1,na,na,na,na,10510,3241409,Bovine adenovirus 3,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40311,MRC Virology Unit,GCF_000885255.1,identical,na,genome length too large,na,2025-07-14,haploid,viral,34446,34446,54.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000857845.1,na,na,na,na,10512,3241412,Canine adenovirus 1,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj15101,MRC Virology Unit,GCF_000857845.1,identical,na,na,na,2025-07-14,haploid,viral,30536,30536,47.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000856885.1,na,na,na,na,10514,3241412,Canine adenovirus 2,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj15102,MRC Virology Unit,GCF_000856885.1,identical,na,na,na,2025-07-14,haploid,viral,31323,31323,50.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000859465.1,na,na,na,na,10515,3241411,Human adenovirus 2,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj15106,MRC Virology Unit,GCF_000859465.1,identical,na,na,na,2025-07-14,haploid,viral,35937,35937,55.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000859485.1,na,na,na,na,10519,3241406,Human adenovirus 7,na,na,suppressed,Complete Genome,Major,Full,2004-09-28,ViralProj15114,MRC Virology Unit,GCF_000859485.1,identical,na,na,na,2025-07-14,haploid,viral,35514,35514,51.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2004-09-28,na,na,na,15448340
GCA_000857885.1,na,na,na,na,10522,3241406,Human adenovirus 35,na,na,suppressed,Complete Genome,Major,Full,2004-09-28,ViralProj15115,MRC Virology Unit,GCF_000857885.1,identical,na,na,na,2025-07-14,haploid,viral,34794,34794,49.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2004-09-28,na,na,na,15448340
GCA_000885275.1,na,na,na,na,10530,3241422,Murine adenovirus 1,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40319,MRC Virology Unit,GCF_000885275.1,identical,na,na,na,2025-07-14,haploid,viral,30944,30944,48.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000858645.1,na,na,na,na,10533,3241411,Human adenovirus 1,na,na,suppressed,Complete Genome,Major,Full,2004-09-28,ViralProj15113,MRC Virology Unit,GCF_000858645.1,identical,na,na,na,2025-07-14,haploid,viral,36001,36001,55.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2004-09-28,na,na,na,15448340
GCA_000884315.1,na,na,na,na,10553,3426541,Fowl aviadenovirus 1,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40323,MRC Virology Unit,GCF_000884315.1,identical,na,na,na,2025-07-14,haploid,viral,43804,43804,54.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_039321755.1,na,na,na,na,11320,2955291,Influenza A virus,strain=A/chicken/China/HN22/2022,HN22,replaced,Complete Genome,Major,Full,2023-12-25,ASM3932175v1,517, Henan Agricultural University,na,na,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/039/321/755/GCA_039321755.1_ASM3932175v1,na,na,2025-06-03,haploid,viral,13361,13361,44.000000,8,8,8,517, Henan Agricultural University,Annotation submitted by 517, Henan Agricultural University,2023-12-30,12,12,0,na
GCA_049891795.1,PRJNA806906,na,na,na,11320,2955291,Influenza A virus,strain=A/lesser scaup/Ohio/23OS0403/2023,na,suppressed,Complete Genome,Major,Full,2025-04-22,ASM4989179v1,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),na,na,na,na,na,2025-07-18,haploid,viral,13127,13127,44.500000,8,8,8,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),Annotation submitted by NIAID Centers of Excellence for Influenza Research and Response (CEIRR),2025-04-22,12,12,0,na
GCA_049891805.1,PRJNA806906,na,na,na,11320,2955291,Influenza A virus,strain=A/lesser scaup/Ohio/23OS0412/2023,na,suppressed,Complete Genome,Major,Full,2025-04-22,ASM4989180v1,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),na,na,na,na,na,2025-07-18,haploid,viral,13127,13127,44.500000,8,8,8,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),Annotation submitted by NIAID Centers of Excellence for Influenza Research and Response (CEIRR),2025-04-22,12,12,0,na
GCA_049891815.1,PRJNA806906,na,na,na,11320,2955291,Influenza A virus,strain=A/lesser scaup/Ohio/23OS0433/2023,na,suppressed,Complete Genome,Major,Full,2025-04-22,ASM4989181v1,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),na,na,na,na,na,2025-07-18,haploid,viral,13136,13136,44.500000,8,8,8,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),Annotation submitted by NIAID Centers of Excellence for Influenza Research and Response (CEIRR),2025-04-22,12,12,0,na
GCA_049891825.1,PRJNA806906,na,na,na,11320,2955291,Influenza A virus,strain=A/lesser scaup/Ohio/23OS0442/2023,na,suppressed,Complete Genome,Major,Full,2025-04-22,ASM4989182v1,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),na,na,na,na,na,2025-07-18,haploid,viral,13136,13136,44.500000,8,8,8,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),Annotation submitted by NIAID Centers of Excellence for Influenza Research and Response (CEIRR),2025-04-22,12,12,0,na
GCA_049909625.1,PRJNA806906,na,na,na,11320,2955291,Influenza A virus,strain=A/lesser scaup/Ohio/23OS0327/2023,na,suppressed,Complete Genome,Major,Full,2025-04-23,ASM4990962v1,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),na,na,na,na,na,2025-07-18,haploid,viral,13127,13127,44.500000,8,8,8,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),Annotation submitted by NIAID Centers of Excellence for Influenza Research and Response (CEIRR),2025-04-23,12,11,0,na
GCA_049909635.1,PRJNA806906,na,na,na,11320,2955291,Influenza A virus,strain=A/lesser scaup/Ohio/23OS0357/2023,na,suppressed,Complete Genome,Major,Full,2025-04-23,ASM4990963v1,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),na,na,na,na,na,2025-07-18,haploid,viral,13136,13136,44.500000,8,8,8,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),Annotation submitted by NIAID Centers of Excellence for Influenza Research and Response (CEIRR),2025-04-23,12,12,0,na
GCA_049909645.1,PRJNA806906,na,na,na,11320,2955291,Influenza A virus,strain=A/lesser scaup/Ohio/23OS0410/2023,na,suppressed,Complete Genome,Major,Full,2025-04-23,ASM4990964v1,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),na,na,na,na,na,2025-07-18,haploid,viral,13130,13130,44.500000,8,8,8,NIAID Centers of Excellence for Influenza Research and Response (CEIRR),Annotation submitted by NIAID Centers of Excellence for Influenza Research and Response (CEIRR),2025-04-23,12,12,0,na
GCA_000884295.1,na,na,na,na,28282,3241402,Human adenovirus 12,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40315,MRC Virology Unit,GCF_000884295.1,identical,na,na,na,2025-07-14,haploid,viral,34125,34125,46.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000857865.1,na,na,na,na,28285,3241411,Human adenovirus 5,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj15107,MRC Virology Unit,GCF_000857865.1,identical,na,na,na,2025-07-14,haploid,viral,35938,35938,55.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000849745.1,na,na,na,na,35265,3241441,Porcine adenovirus 3,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj14610,MRC Virology Unit,GCF_000849745.1,identical,na,na,na,2025-07-14,haploid,viral,34094,34094,64.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000856905.1,na,na,na,na,41678,3241306,Turkey adenovirus 3,na,na,suppressed,Chromosome,Major,Partial,2003-08-16,ViralProj15112,MRC Virology Unit,GCF_000856905.1,identical,na,partial,na,2025-07-14,haploid,viral,26263,26263,35.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000885915.1,na,na,na,na,45370,3241440,Porcine adenovirus 5,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40317,MRC Virology Unit,GCF_000885915.1,identical,na,na,na,2025-07-14,haploid,viral,32621,32621,50.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000858625.1,na,na,na,na,46922,3241420,Human adenovirus 17,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj15105,MRC Virology Unit,GCF_000858625.1,identical,na,na,na,2025-07-14,haploid,viral,35100,35100,56.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000848065.1,na,na,na,na,47680,3241451,Tree shrew adenovirus 1,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj14611,MRC Virology Unit,GCF_000848065.1,identical,na,na,na,2025-07-14,haploid,viral,33501,33501,50.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000885895.1,na,na,na,na,114429,3241410,Bovine adenovirus 2,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40309,MRC Virology Unit,GCF_000885895.1,identical,na,na,na,2025-07-14,haploid,viral,33034,33034,43.500000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000847265.1,na,na,na,na,129953,3241408,Bovine mastadenovirus A,na,na,suppressed,Complete Genome,Major,Full,2004-09-28,ViralProj14612,MRC Virology Unit,GCF_000847265.1,identical,na,na,na,2025-07-14,haploid,viral,34185,34185,49.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2004-09-28,na,na,na,15448340
GCA_000886775.1,na,na,na,na,130329,3426632,Duck adenovirus 1,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40313,MRC Virology Unit,GCF_000886775.1,identical,na,na,na,2025-07-14,haploid,viral,33213,33213,43.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000886795.1,na,na,na,na,172864,3426525,Fowl adenovirus 9,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj40321,MRC Virology Unit,GCF_000886795.1,identical,na,na,na,2025-07-14,haploid,viral,45063,45063,54.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000848905.1,na,na,na,na,175567,3241425,Simian adenovirus 25,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj14608,MRC Virology Unit,GCF_000848905.1,identical,na,na,na,2025-07-14,haploid,viral,36519,36519,59.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_000847245.1,na,na,na,na,198503,3241406,simian adenovirus 21,na,na,suppressed,Complete Genome,Major,Full,2003-08-16,ViralProj14607,MRC Virology Unit,GCF_000847245.1,identical,na,na,na,2025-07-14,haploid,viral,35524,35524,51.000000,1,1,1,MRC Virology Unit,Annotation submitted by MRC Virology Unit,2003-10-24,na,na,na,14573794
GCA_002966475.2,na,na,na,na,2126984,3060757,Tupanvirus deep ocean,na,deep ocean,replaced,Chromosome,Major,Partial,2020-06-17,Tupan virus deep ocean,Microbiologia, UFMG,GCF_002966475.1,identical,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/966/475/GCA_002966475.2_Tupan_virus_deep_ocean,partial,na,2025-06-26,haploid,viral,1439508,1439487,29.500000,1,1,1,Microbiologia, UFMG,Annotation submitted by Microbiologia, UFMG,2020-06-17,na,na,na,29487281
GCA_002966485.2,na,na,na,na,2126985,3060758,Tupanvirus soda lake,na,soda lake,replaced,Chromosome,Major,Full,2020-06-17,Tupanvirus,Microbiologia, UFMG,GCF_002966485.1,identical,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/966/485/GCA_002966485.2_Tupanvirus,na,na,2025-06-26,haploid,viral,1516267,1515867,29.000000,1,1,1,Microbiologia, UFMG,Annotation submitted by Microbiologia, UFMG,2020-06-17,na,na,na,29487281
---- 30 removed because presumed guilt ----
GCA_049891805.1 Influenza A virus strain=A/lesser scaup/Ohio/23OS0412/2023 ASM4989180v1
GCA_049891795.1 Influenza A virus strain=A/lesser scaup/Ohio/23OS0403/2023 ASM4989179v1
GCA_049891815.1 Influenza A virus strain=A/lesser scaup/Ohio/23OS0433/2023 ASM4989181v1
GCA_049891825.1 Influenza A virus strain=A/lesser scaup/Ohio/23OS0442/2023 ASM4989182v1
GCA_049909645.1 Influenza A virus strain=A/lesser scaup/Ohio/23OS0410/2023 ASM4990964v1
GCA_049909635.1 Influenza A virus strain=A/lesser scaup/Ohio/23OS0357/2023 ASM4990963v1
GCA_049909625.1 Influenza A virus strain=A/lesser scaup/Ohio/23OS0327/2023 ASM4990962v1
GCA_029376435.2 Ralstonia phage BOESR1 ASM2937643v1
GCA_000885915.1 Porcine adenovirus 5, ViralProj40317
GCA_000848065.1 Tree shrew adenovirus 1, ViralProj14611
GCA_000848905.1 Simian adenovirus 25, ViralProj14608
GCA_000857865.1 Human adenovirus 5, ViralProj15107
GCA_000857845.1 Canine adenovirus 1, ViralProj15101
GCA_000856905.1 Turkey adenovirus 3, ViralProj15112
GCA_000859465.1 Human adenovirus 2, ViralProj15106
GCA_000886775.1 Duck adenovirus 1, ViralProj40313
GCA_000884295.1 Human adenovirus 12, ViralProj40315
GCA_000884315.1 Fowl aviadenovirus 1, ViralProj40323
GCA_000858625.1 Human adenovirus 17, ViralProj15105
GCA_000886795.1 Fowl aviadenovirus 9, ViralProj40321
GCA_000856885.1 Canine adenovirus 2, ViralProj15102
GCA_000859485.1 Human adenovirus 7, ViralProj15114
GCA_000849745.1 Porcine adenovirus 3, ViralProj14610
GCA_000885275.1 Murine adenovirus 1, ViralProj40319
GCA_000847265.1 Bovine mastadenovirus A, ViralProj14612
GCA_000857885.1 Human adenovirus 35, ViralProj15115
GCA_000885255.1 Bovine adenovirus 3, ViralProj40311
GCA_000858645.1 Human adenovirus 1, ViralProj15113
GCA_000885895.1 Bovine adenovirus 2, ViralProj40309
GCA_000847245.1 Simian adenovirus 21, ViralProj14607
---- 3 removed because version changed ----
GCA_039321755.1 Influenza A virus strain=A/chicken/China/HN22/2022 ASM3932175v1
GCA_002966485.2 Tupanvirus soda lake, ASM296648v2
GCA_002966475.2 Tupanvirus deep ocean, ASM296647v2When checking the final database, there are -1 missed signatures of the expected 239505.
Expand for details
Genomes failed to download or sketch
The sourmash plugin DirectSketch was used to download and sketch the missing or updated genomes. This plugin failed to download 0 sequences.
Expand for details
accession,name,moltype,md5sum,download_filename,url,rangeWithin the workflow-cleanup directory, there are files for manually downloading any missing genomes and manually checking the remaining genomes.
Expand for commands
Consider running:
cd /group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806
sourmash scripts gbsketch workflow-cleanup/manual-download.20250806-viral.csv -o workflow-cleanupmanual-download.20250806-viral.zip --failed workflow-cleanup/manual-download.20250806-viral.failed.csv --param-str "dna,ksize=21,ksize=31,ksize=51,scaled=1000,abund" -r 5 -g 2> workflow-cleanup/manual-download.20250806-viral.log
mv genbank-20250806-viral-k21.zip genbank-20250806-viral-k31.zip genbank-20250806-viral-k51.zip workflow-cleanup/ && cd workflow-cleanup/
sourmash sig cat manual-download.20250806-viral.zip genbank-20250806-viral-k21.zip -k 21 -o ../genbank-20250603-viral-k21.zip
sourmash sig cat manual-download.20250806-viral.zip genbank-20250806-viral-k31.zip -k 31 -o ../genbank-20250603-viral-k31.zip
sourmash sig cat manual-download.20250806-viral.zip genbank-20250806-viral-k51.zip -k 51 -o ../genbank-20250603-viral-k51.zipDetails below:
awk: fatal: cannot open file `/group/ctbrowngrp4/2024-ccbaumler-genbank/genbank-20250806/data/mf-updated-versions.20250806-viral.csv' for reading: No such file or directory
Recovered 0/0 missing genomes for manual download and addition to the viral database
The remaining 0 missing genomes must be manually checked and may be suspended genomes
There are 0 duplicates in the manual-download.20250806-viral.csv file
Check the report files for more information on the suspended genomes most likely missing from the final database
Expand for manual-download.20250806-viral.csv details:
accession,name,ftp_path
Expand for manual-check.20250806-viral.csv details: