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guille0387 avatar guille0387 commented on July 3, 2024 1

Hi @hoelzer @Ales-ibt

Yes, I think it should be possible to invert the order of the ranks and include the complete lineage.... let me have a look into this and I'll get back to you asap.

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hoelzer avatar hoelzer commented on July 3, 2024

Hey, thx @Ales-ibt !

Yes agree, inverting the ranks would make more sense probably. Having the full ranks shown should be also possible with the NCBI taxonomy file @guille0387 , or?

Regarding the Caudovirales vs Caudoviricetes: actually Caudovirales should not be in the pipeline anymore bc the taxa was discontinued by ICTV. We added the following warning mssg when running VIRify:

Warning: --meta_version v4 does not include the following discontinued virus taxa 
(according to ICTV) anymore and they have been excluded from the dataset.
- Allolevivirus
- Autographivirinae
- Buttersvirus
- Caudovirales
- Chungbukvirus
- Incheonvirus
- Leviviridae
- Levivirus
- Mandarivirus
- Pbi1virus
- Phicbkvirus
- Radnorvirus
- Sitaravirus
- Vidavervirus
- Myoviridae
- Siphoviridae
- Podoviridae
- Viunavirus
- Orthohepevirus
- Klosneuvirus
- Hendrixvirus
- Rubulavirus
- Avulavirus
- Catovirus
- Nucleorhabdovirus
- Viunavirus
- Gammalipothrixvirus
- Peduovirinae
- Sedoreovirinae

Did you still had Caudovirales in your results? Can you try a fresh installation and most importantly re-download of the database files? Maybe an old database file was still used.

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guille0387 avatar guille0387 commented on July 3, 2024

Hi @hoelzer @Ales-ibt

I created a new branch called out_lineage with modifications in the contig taxonomic assignment script. The output should now reflect the suggestions that Ales made. I tested it with the two mock datasets we used in the paper and it worked, but perhaps Ales would like to try it with her own data? Let me know if you have any issues.

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hoelzer avatar hoelzer commented on July 3, 2024

Great, thx @guille0387 ! Looks also good for me. @Ales-ibt can you give it a try as well? thx!

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Ales-ibt avatar Ales-ibt commented on July 3, 2024

Great, I'll run a test and be back to you soon.

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Ales-ibt avatar Ales-ibt commented on July 3, 2024

Hello, sorry about taking that long to be back. I updated the NCBI database and now I have the correct Caudoviricetes annotation :D. I also tested the pipeline on the out_lineage branch and I can see the complete lineages beautifully sorted on the 08-final/taxonomy/*prodigal_annotation_taxonomy.tsv, thank you so much for this. The only detail is that this fix is not reflected on the GFF output file.

Thank you again!

Ales

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hoelzer avatar hoelzer commented on July 3, 2024

Awesome, thanks for checking, @Ales-ibt !

@guille0387 can you also do the GFF fix and then we could merge that into dev @mberacochea

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mberacochea avatar mberacochea commented on July 3, 2024

Excellent @guille0387!, thank you for that fix. Let me know if you need a hand fixing the GFF.

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guille0387 avatar guille0387 commented on July 3, 2024

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