My understanding is that the bias value of the hmmscan output is supposed to rage between 0 and 1:
Bias - The bias composition correction (ranging between 0 and 1), is the bit score difference contributed by the null2 model. High bias scores may be a red flag for a false positive. It is difficult to correct for all possible ways in which nonrandom but nonhomologous biological sequences can appear to be similar, such as short-period tandem repeats, so there are cases where the bias correction is not strong enough (creating false positives).
However for many hits that I am seeing against the PfamA database, I see biases above 1 for both the "full sequence" and "this domain" categories. Am I missing something?
Here's the command I used
hmmscan -domtblout <out fi> -cpu 22 PfamA.hmm <input data> > hmmscan.log
The version is 3.1b1