DESeq2 error using HTseq count


I am trying to run DESeq2 using HTseq count as input but I am running in the following error every time, I already checked and input data is correct.

Error in Ops.factor(a$V1, l[[1]]$V1) :
level sets of factors are different
Calls: DESeqDataSetFromHTSeqCount -> sapply -> sapply -> lapply -> FUN -> Ops.factor
Warning message:
In | :
longer object length is not a multiple of shorter object length

I have 4 replicates per treatment (two treatments) and they have different number of lines (outpu htseq) but I think this is normal since htseq counts the number of exons and they could be different among replicates.

I read that the problem could be the gff3 format but the annotation of the genome is not in gtf format. Is there a tool in Galaxy to do the conversion?.

Thank you very much in advance,