I am trying to fetch promoter sequences from a bacterial genome, retrieving only those sequences that don't fall into cds. I think the problem is that some sequences fall out of the FASTA sequences (2 chromosomes, 2 plasmids) that are not recognized as circular giving me an error from scanFa.

Here there's my code

phy<-makeTxDbFromGFF(file.choose(),format = "auto")


GR <- cdsBy(phy,"tx",use.names=TRUE)
indexFa(file.choose())
phy.fasta<-FaFile(file.choose(), index=sprintf("%s.fai", file.choose()))

p<-promoters(phy,200,0)
promoter_seqs<-subsetByOverlaps(p,GR,invert = TRUE)
promoter_seqs <- scanFa(phy.fasta,promoter_seqs,use.names=TRUE)

this is the error I get from scanFa:

Error in value[[3L]](cond) : 
record 1470 (1:3479165-3479364) was truncated

this is the seqinfo of phy.fasta

seqinfo(phy.fasta)
Seqinfo object with 4 sequences from an unspecified genome:
  seqnames seqlengths isCircular genome
  pBPHY01     1904893         NA   <NA>
  pBPHY02      595108         NA   <NA>
  1           3479187         NA   <NA>
  2           2697374         NA   <NA>

I have tried also with isCircular but this method doesn't work with FAfile

I hope that I have been clear, and thanks in advance for your time and your precious advises!