Compatibility with VIRGO2 outputs

[lauravega-29]

I would like to confirm whether the tool is compatible with outputs from VIRGO2. I am encountering an issue where the VIRGO IDs change between different VIRGO versions. Specifically, when running the lines from classify_mgCST_centroid.R:
genes<-merge(gene.length, taxon.tbl[,c("VIRGO_ID", "Taxa")], all=TRUE, by="VIRGO_ID")
genes<-merge(genes, counts.genes, all.y=TRUE, by="VIRGO_ID")
This produces a table with Taxa as NA. As a result, NAs appear that prevent mgCST classification. I would appreciate any support on this issue. Thank you!

[jbholm]

Hi Laura, We have a new mgCST classifier for VIRGO2, VISTA: Access it here: https://github.com/JHolm-Lab/VISTA This is compatible with VIRGO2. Best, Johanna

…

------------------------------------------ Johanna B. Holm, PhD Assistant Professor Department of Microbiology & Immunology Center for Advance Microbiome Research & Innovation (CAMRI) Institute for Genome Sciences (IGS) 670 W. Baltimore Street, Rm 3176 University of Maryland Baltimore, School of Medicine ☏: 410-706-7905 ***@***.******@***.***> From: lauravega-29 ***@***.***> Date: Thursday, January 22, 2026 at 10:22 AM To: ravel-lab/mgCST-classifier ***@***.***> Cc: Subscribed ***@***.***> Subject: [ravel-lab/mgCST-classifier] Compatibility with VIRGO2 outputs (Issue #1) [https://avatars.githubusercontent.com/u/73129539?s=20&v=4]lauravega-29 created an issue (ravel-lab/mgCST-classifier#1)<#1> I would like to confirm whether the tool is compatible with outputs from VIRGO2. I am encountering an issue where the VIRGO IDs change between different VIRGO versions. Specifically, when running the lines from classify_mgCST_centroid.R: genes<-merge(gene.length, taxon.tbl[,c("VIRGO_ID", "Taxa")], all=TRUE, by="VIRGO_ID") genes<-merge(genes, counts.genes, all.y=TRUE, by="VIRGO_ID") This produces a table with Taxa as NA. As a result, NAs appear that prevent mgCST classification. I would appreciate any support on this issue. Thank you! — Reply to this email directly, view it on GitHub<#1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEC7OTK6OMG35JDJDK72MYD4IDTKRAVCNFSM6AAAAACSRVUBN6VHI2DSMVQWIX3LMV43ASLTON2WKOZTHA2DGNBSG4ZDMNQ>. You are receiving this because you are subscribed to this thread.