Clarification of is_phage Values (−1, 0, 1) in Phager Output for Archaeal Genomes

[linweiliarchaea]

Dear phager developers @AnastasiyaGaede @tsp-kucbd ,

We ran phager on a set of archaeal genomes and obtained the following output (excerpt shown below):

contig (runtime:24 seconds)  name    genes   is_phage    score   bp
0   NZ_CAYLEQ010000004.1     80      0       0.14    89261.0
1   NZ_CAYLEQ010000003.1     110     0       0.2     100540.0
...
18  NZ_CAYLEQ010000019.1     25      1       0.96    26321.0
...
36  NZ_CAYLEQ010000040.1     4       -1      0.25    8045.0
...
44  NZ_CAYLEQ010000046.1     0       -1      -1.0    -1.0
...
49  NZ_CAYLEQ010000050.1     6       0       0.0     5519.0

We would appreciate clarification regarding the interpretation of the is_phage column. In particular, this field appears to take three distinct values: -1, 0, and 1.

Could you please clarify:

1. The biological and/or computational meaning of each of these values (i.e., what exactly do -1, 0, and 1 represent in terms of phage classification)?

2. Under what circumstances a contig is assigned is_phage = -1, especially in comparison to 0 (non-phage) and 1 (phage)?

3. Whether -1 indicates insufficient information, filtering due to contig length or gene count, or a failed/unsupported prediction case?

Understanding these distinctions would greatly help us interpret the results correctly, especially for archaeal genomes, where prophage detection can be more challenging.

Thank you very much for your time and for developing and maintaining Phager.

Best regards,
Lily