patch output genome is identical to input target genome

[wackerk]

Hello! I am attempting to patch a scaffold-assembled reference genome of a congener of my focal bird species (TANG, in the code below) with a chromosome-level reference genome of a more distantly related species (CAMAR, in the code below). I ran RagTag with default settings and the stderr output file tracking the progress showed that the program worked appropriately. However, when I use QUAST to compare the original scaffold reference (TANG) with the patched reference, results indicate that the genomes are identical (same # contigs, N50, L50, etc). Any ideas on what has happened? An issue with using default settings perhaps?

Code used for RagTag:

RAGTAG=/home/kwacker/RagTag/ragtag.py
TANG=/nfs/turbo/lsa-wingerb1/kswacker/tangara_popgen/ref_genomes/tang/tang_gyr_ref.fasta
CAMAR=/nfs/turbo/lsa-wingerb1/kswacker/tangara_popgen/ref_genomes/camar/GCA_901933205.1_STF_HiC_genomic.fna
OUT=/nfs/turbo/lsa-wingerb1/kswacker/tangara_popgen/ref_genomes/tang_patch/
NUCMER=/home/kwacker/anaconda3/bin/nucmer

$RAGTAG patch $TANG $CAMAR -u -o $OUT --aligner $NUCMER

I would also add that I used QUAST to compare my original scaffold reference (TANG) and the original chromosome reference (CAMAR), and found that the chromosome-level genome assembly was much better as expected. So I don't believe the issue is that I'm incorrectly running QUAST.

Thanks in advance for any ideas you might have!