Invalid node

[maxedge420]

I downloaded some RefSeq sequences, new_taxdump and nucl_wgs.accession2taxid to try and create a database. In the end (after a day of DB creating) I got the following messages:

Merge reference DB files ...
Invalid node 3384601!

When I try to use the DB to classify, i just get

Invalid node 3384601!

I assumed it was signaling about the nodes from new_taxdump, and a quick search revealed node 3384601 is only present inside delnodes.dmp, if that means anything.

Any suggestions on what to do?

[jaebeom-kim]

Could you kindly provide the Metabuli version you used?
You can see it when you just run metabuli without any command.

Metabuli is a taxonomical classifier that jointly analyzes amino acid and DNA sequences.

metabuli Version: HERE YOU CAN SEE THE VERSION
© Jaebeom Kim <[email protected]>

usage: metabuli <command> [<args>]

Main workflows for database input/output
  classify          	Assigning taxonomy label to query reads
  extract           	It extracts reads classified into a certain taxon. It should be used after classification.

Input database creation
  databases         	List and download databases
  build             	Build database based on the list of FASTA files.
  updateDB          	Add new sequences to the database

Format conversion for downstream processing
  binning2report    	It generates Kraken style report file from binning results

An extended list of all modules can be obtained by calling 'metabuli -h'.

[maxedge420]

Version 1.0.9.2, installed from conda.

[jaebeom-kim]

Could you test the latest commit in this repo?
I would recommend testing with a subset of sequences first before running with the entire sequences.

[maxedge420]

Thank you for the timely replies. Metabuli 1.0.8 gave me this warning at the start:

Cannot find accession: NC_029549.1
Please run 'add-to-library' first.

I thought metabuli just skipped missing accessions.

[jaebeom-kim]

Sorry for my ambiguous answer.
I meant use the latest source code to compile Metabuli.
Here is how to: https://github.com/steineggerlab/Metabuli?tab=readme-ov-file#compile-from-source-code