Does prediction with no coordinates indicate the whole sequences is a viral sequence?

[shenwei356]

I just found the answer:

coordinates: 1-indexed coordinates of the provirus region within host sequences. Will be NA for viruses that were not predicted to be integrated.

Normal prediction result.

seq_name               length   topology   coordinates     n_genes   genetic_code   virus_score   fdr   n_hallmarks   marker_enrichment   taxonomy            
--------------------   ------   --------   -------------   -------   ------------   -----------   ---   -----------   -----------------   --------------------
CP000388.1|provirus_   52034    Provirus   774617-826650   58        11             0.9401        NA    11            45.1836             Viruses;            
774617_826650                                                                                                                             Duplodnaviria;      
                                                                                                                                          Heunggongvirae;     
                                                                                                                                          Uroviricota;        
                                                                                                                                          Caudoviricetes

Prediction without coordinates (genome is GCA_000166735.2, a MAG).

seq_name         length   topology              coordinates   n_genes   genetic_code   virus_score   fdr   n_hallmarks   marker_enrichment   taxonomy            
--------------   ------   -------------------   -----------   -------   ------------   -----------   ---   -----------   -----------------   --------------------
AEMJ01000831.1   698      No terminal repeats   NA            1         11             0.9638        NA    0             1.7183              Viruses;            
                                                                                                                                             Duplodnaviria;      
                                                                                                                                             Heunggongvirae;     
                                                                                                                                             Uroviricota;        
                                                                                                                                             Caudoviricetes      
AEMJ01000737.1   1746     No terminal repeats   NA            2         11             0.9244        NA    0             1.7183              Viruses;            
                                                                                                                                             Duplodnaviria;      
                                                                                                                                             Heunggongvirae;     
                                                                                                                                             Uroviricota;        
                                                                                                                                             Caudoviricetes      
AEMJ01000706.1   826      No terminal repeats   NA            1         11             0.8908        NA    0             1.4495              Viruses;            
                                                                                                                                             Duplodnaviria;      
                                                                                                                                             Heunggongvirae;     
                                                                                                                                             Uroviricota;        
                                                                                                                                             Caudoviricetes      
AEMJ01000847.1   3369     No terminal repeats   NA            2         11             0.8785        NA    0             1.7183              Viruses;            
                                                                                                                                             Duplodnaviria;      
                                                                                                                                             Heunggongvirae;     
                                                                                                                                             Uroviricota;        
                                                                                                                                             Caudoviricetes      
AEMJ01000526.1   288      No terminal repeats   NA            2         11             0.8497        NA    0             0.0000              Unclassified        
AEMJ01000792.1   2672     No terminal repeats   NA            3         11             0.8414        NA    0             1.7183              Unclassified        
AEMJ01000320.1   1885     No terminal repeats   NA            2         11             0.8297        NA    0             1.7183              Unclassified        
AEMJ01000546.1   283      No terminal repeats   NA            2         11             0.8262        NA    0             0.0000              Unclassified        
AEMJ01000712.1   349      No terminal repeats   NA            2         11             0.8238        NA    0             0.0000              Unclassified

$ seqkit stats GCA_000166735.2.fna.gz 
file                    format  type  num_seqs    sum_len  min_len  avg_len  max_len
GCA_000166735.2.fna.gz  FASTA   DNA        893  2,298,088      101  2,573.4   82,336

$ seqkit seq -n GCA_000166735.2.fna.gz | head -n 3
AEMJ01000893.1 UNVERIFIED_ORG: Leuconostoc inhae KCTC 3774 contig00909, whole genome shotgun sequence
AEMJ01000892.1 UNVERIFIED_ORG: Leuconostoc inhae KCTC 3774 contig00908, whole genome shotgun sequence
AEMJ01000891.1 UNVERIFIED_ORG: Leuconostoc inhae KCTC 3774 contig00907, whole genome shotgun sequence

[apcamargo]

Good that you already found the answer :)

As a note, be careful with those very short sequences. In particular with the ones without markers. I usually require a hallmark for the short ones.

[shenwei356]

I forgot to say that I used the --relaxed flag.

Thanks for the message. :)