[github-actions]

Automated monthly update for HerpesDRG source data.

• Previous source date: 2026-07-05
• Source commit date: 2026-09-29
• Source commit SHA: 22fc18676a1ea49cd6d7cd1c3280db210a7580e6
• Source URL: https://raw.githubusercontent.com/ojcharles/herpesdrg-db/main/herpesdrg-db.tsv

respro build QC

Source: herpesdrg
Status: ⚠️ respro init succeeded with 1 skipped rule(s).
Exit code: 0
Imported single rules: 2779
Imported formula rules: 3
Skipped — reference AA mismatch: 1
Skipped — feature not in GenBank: 0
Skipped — formula member missing: 0

Raw respro init output

[2026-10-01 16:16:00] WARNING  respro.io.genbank — Skipping duplicate CDS 'ORF64' in 'NC_001348.1' (already loaded; likely present in both copies of an inverted
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'ORF63' in 'NC_001348.1' (already loaded; likely present in both copies of an inverted
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'ORF62' in 'NC_001348.1' (already loaded; likely present in both copies of an inverted
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'DR1' in 'NC_001664.4' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'DR6' in 'NC_001664.4' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'RL2' in 'NC_001798.2' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'RL1' in 'NC_001798.2' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'RS1' in 'NC_001798.2' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'RL2' in 'NC_001806.2' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'RL1' in 'NC_001806.2' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      WARNING  respro.io.genbank — Skipping duplicate CDS 'RS1' in 'NC_001806.2' (already loaded; likely present in both copies of an inverted  
                               repeat region).                                                                                                                  
                      INFO     respro.db.features — Loaded GenBank data: references +6 (reused 0), features +509 (reused 0)                                     
                      INFO     respro.db.rules_import — Detected 1-based amino acid positions in rules TSV                                                      
                      WARNING  respro.db._rules_features — 1 position(s) with rules have reference AA mismatches and will be skipped:                           
                                 NC_001664 feature 'U69' pos 462 (1-based): rule says 'A', feature sequence has 'C' — rule will be skipped                      
                      INFO     respro.db.rules_import — Loaded 2779 single resistance rule(s)                                                                   
                      INFO     respro.db.rules_import — Loaded 3 formula resistance rule(s)                                                                     
                      WARNING  respro.db.algorithms — Algorithm config declares phenotype label 'high-level resistance', which is not among the labels stored in
                               the database (['contradictory', 'resistant', 'sensitive']). The label still resolves to a rank and processing continues; verify  
                               the vocabulary is consistent between the algorithm config and the rules sheet.                                                   
                      WARNING  respro.db.algorithms — Algorithm config declares phenotype label 'intermediate', which is not among the labels stored in the     
                               database (['contradictory', 'resistant', 'sensitive']). The label still resolves to a rank and processing continues; verify the  
                               vocabulary is consistent between the algorithm config and the rules sheet.                                                       
                      WARNING  respro.db.algorithms — Algorithm config declares phenotype label 'low-level resistance', which is not among the labels stored in 
                               the database (['contradictory', 'resistant', 'sensitive']). The label still resolves to a rank and processing continues; verify  
                               the vocabulary is consistent between the algorithm config and the rules sheet.                                                   
                      WARNING  respro.db.algorithms — Algorithm config declares phenotype label 'susceptible', which is not among the labels stored in the      
                               database (['contradictory', 'resistant', 'sensitive']). The label still resolves to a rank and processing continues; verify the  
                               vocabulary is consistent between the algorithm config and the rules sheet.                                                       
                      INFO     respro.cli.init — Project initialized: herpesdrg (/tmp/respro_qc/herpesdrg.db)                                                   
✓ Project initialised: /tmp/respro_qc/herpesdrg.db

This PR was generated by the autobump workflow.

[jonas-fuchs]

@ojcharles Thanks a lot for the update! Could you give the autobump a quick confirmation from your side if its ok? I have still the problem that I cannot parse some deletions correctly (databases/herpesdrg/output/non-migrated-rules.txt). I can implement logic in the script but without knowing the aminoacids that should be deleted I will not be able to verify the rules.

Moreover, I get one mismatch during db creation (this runs automtically in these PRs as QC):

WARNING respro.db._rules_features — 1 position(s) with rules have reference AA mismatches and will be skipped: NC_001664 feature 'U69' pos 462 (1-based): rule says 'A', feature sequence has 'C' — rule will be skipped