Issue with incorrect virus classification using metabuli binning2report function and suggestion for ICTV taxonomy update

[Enkabloza]

Hi Metabuli team,

First of all, I would like to thank you for such an excellent tool, I really enjoy using it. I’m currently using Metabuli to classify my viral metagenome sequences, and I have been using the viral database provided by Metabuli for my analyses. After running the classification, I obtain a report file that looks like this:

98.6127 39657793 39657793 no rank 0 unclassified
1.3873 557902 166 no rank 1 root
1.3787 554456 812 superkingdom 10239 Viruses
1.2988 522339 0 clade 2731341 Duplodnaviria
1.2988 522339 31 kingdom 2731360 Heunggongvirae
1.2938 520316 0 phylum 2731618 Uroviricota
1.2938 520316 14652 class 2731619 Caudoviricetes
0.5720 230022 229876 genus 2843396 Jouyvirus
0.0003 105 0 species 2844245 Jouyvirus ev017
0.0003 105 105 no rank 2847060 Escherichia phage ev017

After generating this report, I attempt to convert it into a Kraken-style format using the metabuli binning2report function. However, during this conversion, I encounter an issue where the output file no longer includes virus classifications but instead focuses solely on bacteria. The output looks like this:

30.75 1051 1051 no rank 0 unclassified
54.13 1850 485 no rank 1 root
39.88 1363 0 no rank 131567 cellular organisms
39.47 1349 230 superkingdom 2 Bacteria
17.50 598 0 phylum 1224 Pseudomonadota
7.72 264 0 class 28211 Alphaproteobacteria
5.47 187 0 order 356 Hyphomicrobiales
4.27 146 0 family 335928 Xanthobacteraceae
4.04 138 67 genus 6 Azorhizobium
2.08 71 71 species 7 Azorhizobium caulinodans

Why does this issue occur? My goal is to convert my report to Kraken format so that I can eventually transform the files into a BIOM (Biological Observation Matrix) format. This would allow me to combine all my reports into a single file, and then I could use the R phyloseq package to generate various statistics from my samples.

Additionally, I noticed there have been previous requests regarding updating the taxonomy to align with ICTV. I came across two resources that might be helpful:

This one explains how to construct NCBI-style taxdump files for the International Committee on Taxonomy of Viruses (ICTV):
https://github.com/shenwei356/ictv-taxdump

This other resource provides a tutorial on how to build a protein FASTA database for ICTV (though it is adapted for MMseqs2, it might help in building an ICTV viral database for Metabuli):
https://github.com/apcamargo/ictv-mmseqs2-protein-database/blob/master/README.md

Thank you for your time and attention. I hope you have a great start to the week!

Best regards,

[jaebeom-kim]

Thank you so much for the resources of ICTV !! Sounds very useful.

binning2report was implemented for internal use and wasn't maintained well.
I didn't know that it's visible to users.
It doesn't convert metabuli's report to kraken's report, but it converts read-by-read classification to metabuli's report.
I wrote Kraken style report file because I thought metabuli's report is following kraken's style.

Let me check BIOM format and see if I can make a module for the conversion you want.
Thanks again!

[jaebeom-kim]

Thank you so much for the tips !!
I could build a viral DB based on ICVT VMR39.2.
It's available here.
https://hulk.mmseqs.com/jaebeom/vmr39.2/
Could you try this and give feedback?
Thanks again :)

Please use this Metabuli version.
https://github.com/jaebeom-kim/Metabuli
The DB is not compatible to the latest release.

[Lelouchzhu]

Thank you so much for the tips !! I could build a viral DB based on ICVT VMR39.2. It's available here. https://hulk.mmseqs.com/jaebeom/vmr39.2/ Could you try this and give feedback? Thanks again :)

Please use this Metabuli version. https://github.com/jaebeom-kim/Metabuli The DB is not compatible to the latest release.

Thanks for the effort. Out of curiosity I just checked the latest ICTV taxonomy. They now put SARS-CoV-1 and SARS-CoV-2 all into this weird species name Betacoronavirus pandemicum !! Hope you guys dont follow ICTV taxonomy so soon as it is now so confusing...

[Enkabloza]

Thank you very much, Jaebeom. I hope you're having an excellent start to the week, and I appreciate you taking the time to read my comments and share your database. I apologize for the delayed response. On another note, I have downloaded the ICTV VMR39.2 database that you shared.

Currently, I am using this version of Metabuli: Metabuli Version 1.0.8. I have a question: is the version I downloaded different from the one available in this directory? -> https://github.com/jaebeom-kim/Metabuli

Another question: Should I download the nodes.dmp and names.dmp files from here > https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/ or do I need to build my own taxonomy files using TaxonKit and create an ICTV taxdump file?

Thank you again for your help, and I wish you an excellent day!

Best regards

[jaebeom-kim]

Hi! Your comment was very helpful!

Currently, I am using this version of Metabuli: Metabuli Version 1.0.8. I have a question: is the version I downloaded different from the one available in this directory? -> https://github.com/jaebeom-kim/Metabuli

Yes, please use https://github.com/jaebeom-kim/Metabuli when you try the ICTV database. Sorry for this inconvenience. Taxonkit uses the full range of 32 bit integer for taxonomy ID, but Metabuli used only 31 bits, so I made a quick fix in my fork.

Another question: Should I download the nodes.dmp and names.dmp files from here > https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/ or do I need to build my own taxonomy files using TaxonKit and create an ICTV taxdump file?

You don't need to download any dmp files to try the ICTV database.
But, I just shared dmp files in https://hulk.mmseqs.com/jaebeom/vmr39.2/ictv-taxdump/ just in case.

Thanks again!

[jaebeom-kim]

https://github.com/jaebeom-kim/Metabuli is moved to https://github.com/jaebeom-kim/Metabuli/tree/taxid