Chromosomes IDs do not match in the two genomes

[majssssa]

Thank you very much for developing such an excellent software.

When I was using fixchr to make adjustments to the genome, the following log appeared. My command was
fixchr -F P -f -c Rhinella_marina_Bufo-bufo_150.paf -r Rhinella_marina.fasta -q Bufo-bufo_rename_Unmask.fasta --prefix fixchr_

2025-10-28 23:42:31,329 - fixchr - INFO - Reading alignments (fixchr.py:68)
2025-10-28 23:45:54,473 - fixchr - INFO - Selecting homologous chromosomes (fixchr.py:80)
2025-10-28 23:45:54,474 - homchr - WARNING - Chromosomes IDs do not match in the two genomes (func.py:664)
2025-10-28 23:45:54,597 - fixchr - INFO - Checking chromosome direction (fixchr.py:87)
2025-10-28 23:45:54,602 - fixchr - WARNING - Inverting query chromosomes: ['Chr06', 'Chr09'] (fixchr.py:90)
2025-10-28 23:45:56,528 - fixchr - INFO - Writing output files (fixchr.py:104)
2025-10-28 23:46:26,434 - fixchr - INFO - Finished (fixchr.py:119)

I'm quite certain that the homologous chromosome IDs and chromosome numbers of the reference genome and the query genome are the same. I just don't know where the problem lies now.Below is the result I obtained by using "grep '>'" to count the sequence IDs.

grep ">" Bufo-bufo_rename_Unmask.fasta

Chr02
Chr01
Chr03
Chr04
Chr05
Chr06
Chr08
Chr09
Chr07
Chr10
Chr11

grep ">" Rhinella_marina.fasta

Chr01
Chr02
Chr03
Chr04
Chr05
Chr06
Chr09
Chr07
Chr08
Chr10
Chr11