Troubling in patching?

[jun3234]

Hi,

First thanks for this great tool.

I had get a scaffold sequence that some of its contain N bases, called A.scaffold.

and I used contigs from nanopore using 'Necat' tools, called B.contig.

and ran ragtag.py patch --fill-only --aligner minimap2 --mm2-params '-x asm20' A.scaffold B.contig.

The command line would go through without error, and I got output C.patch.fasta

I found that the size of C.patch.fasta always less than A.scaffold?

Is there something important I got missing?

I mean that if gaps in A.scaffold had be filling, the sequences size of A.scaffold should be less than C.patch.fasta.

Thanks