Unable to fill gap with ragtag scaffold and patch

[yipukangda]

Hi,

I have a bactieria genome sequencing data set which contains an previous NGS assemblied contigs(raw data missed) and recently nanopore sequencing data, so I want fill gaps of ngs contigs with nanopore data assembly genome(using flye and get a complete contig), I first use ragtag scaffold module combines NGS contigs with nanopore assembly genome and get a gap filling contig(and with several sites of Ns nearly 50 Kb in sum),

ragtag.py scaffold -r -g 1 -o bac_scaffold nanpore_assm.fa ngs.contigs.fa

Then try to fill these Ns with patch module with or without set --fill-only.

ragtag.py patch -s 100 -w [--fill-only] bac_scaffol/ragtag.scaffold.fasta nanpore_assm.fa -o bac_gap_fill

But both can not eliminate Ns, is there anything wrong with above commands?

Thanks