@corneliusroemer, thank you!
I missed this line. I’ve checked the aligned.fasta (the one that is used as input for the TreeTime) and found this sequence: >Lu’an/5053/2021.
Apparently, the character ’ confuses TreeTime algorithm, so it takes only the second part of the name.
I will try to rename this sequence in all input files and then will start the refine step again.
Best,
Dmitrii