a bug for the last step of merge

[CrawlingSponge]

hi, Thanks for your useful software! When I performed the last step of the merging of two scaffolds with two different references, the "agp"files with the correspond between the pesudochromomes and scaffold, not the original contig ids from the target genome (original). So, the seqs ids of target genome could not be found within the "agp" files.

the log shows like this: RuntimeError: scf00000000 is in /home/xyx/0.assembly/0.ragtag/out_1/ragtag.scaffold.agp but not congtig.fa.

[miangher]

Hi, I have exactly the same problem!