Where to look for the names of viruses that were identified? taxonomic classification ?

[ShevchenkoAlla]

Hi,
I have tried your beautiful tool on some contigs, and I can't find the names of the viruses.
I have a lot of folders and files.

First log file -

findfont: Found a missing font file. Rebuilding cache.
generated new fontManager
Command: /miniconda3/envs/vibrant_env/bin/VIBRANT_run.py -i /FP1/MEGAHIT/final.contigs.fa -folder /home/vch$
Date: 2026-02-04
Start: 01:20:27
End: 02:08:53
Runtime: 48.4 minutes
Program: VIBRANT v1.2.1

4766148 scaffolds were read in.
60088 scaffolds met minimum requirements: at least 1000bp and 4 ORFs.
1747 putative phages were identified.

The folders are -

final.contigs.prodigal.faa final.contigs.prodigal.gff VIBRANT_HMM_tables_parsed_final.contigs VIBRANT_log_annotation_final.contigs.log VIBRANT_results_final.contigs
final.contigs.prodigal.ffn VIBRANT_figures_final.contigs VIBRANT_HMM_tables_unformatted_final.contigs VIBRANT_phages_final.contigs

So, I have checked some of them, but there are no names.

For example -

final.contigs.combined.txt file looks like this:
k127_1000091 flag=1 multi=21.0000 len=2532
k127_2168281 flag=1 multi=8.0000 len=3983
k127_922271 flag=1 multi=7.0000 len=2405
k127_2145666 flag=1 multi=7.0000 len=1623
k127_2974144 flag=1 multi=4.0000 len=2627
k127_4030549 flag=1 multi=7.0000 len=3480
k127_1111252 flag=1 multi=13.0000 len=14681
k127_2744809 flag=1 multi=16.0000 len=2664
k127_1883349 flag=1 multi=9.0000 len=4135
k127_2379443 flag=1 multi=11.0000 len=3642

VIBRANT_genbank_table_final.contigs.tsv has names of proteins- REFSEQ hypothetical protein
hypothetical protein
sp|Q5UQ73|YL509_MIMIV Uncharacterized protein L509
REFSEQ major head protein

final.contigs.phages_combined.gbk file - /organism="k127_4030549 flag=1 multi=7.0000 len=3480"
CDS 159..671
/locus_tag="k127_4030549 flag=1 multi=7.0000 len=3480_1"
/protein_id="K00558"
/product=""DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37]""
/translation="MEAMTKLPDYYMNIFCPLNASIWLPQERKRLILIGTKKPFSISE
PLPANNRLSIKDILEKDPQVDIPNYVISRLKGKYRDMPIIIDPEDKNAIAPTCVAHYA
KDLGTRLVKDPSFKHGVRPFTIREYARLQGFPDDFKFENNRNSYKLIGNAVGVDMGRW
IGNEALKYFN*"
so instead of the name of viruses - the name of organism is just the id of the contig...

According to your explanations ut should be in mixed_example.faa - MH552500.1 CrAssphage sp. isolate ctcc615, complete genome_1 # , >MK064567.1 Sulfolobus polyhedral virus 2 clone F, - but in my file there ia only contig id's

same picture in K06400 spoIVCA; site-specific DNA recombinase - in your example - in scaffold column there are names - MK064567.1 Sulfolobus polyhedral virus 2 clone F, but in mine tables are only contig names

I also got some err file which showed -

/home/miniconda3/envs/vibrant_env/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:30: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
method='lar', copy_X=True, eps=np.finfo(np.float).eps,
/home/miniconda3/envs/vibrant_env/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:167: DeprecationWarning: np.float is a deprecated alias for the builtin float. To silence this warning, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
method='lar', copy_X=True, eps=np.finfo(np.float).eps,

Is this could be the reason that there are no names of identified viruses?

Thanks