That sort of error could be caused by one of the files in the .d folder being corrupted.
If you send us all of the files in that .d folder we could tell you what seems to be going wrong.
It would be best if you could package everything up into a .zip file.
Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url
-- Nick

Hi Nick,

Thank you for your response, I just uploaded one of .d file to the link. (SILpeptides_1aM_E14_GE15_1_4495.d)
Please delete it after you download.
Thank you.

Best regards,
Jihyeon

Thank you for uploading that file.
Yes, the file "analysis.tdf" appears to be corrupted.

There is a program called "sqlite3.exe" which can be used to check whether a database file such as "analysis.tdf" is corrupted.

When I run:
sqlite3.exe analysis.tdf "PRAGMA integrity_check;"

I get the output:

*** in database main ***
On tree page 23 cell 0: invalid page number 4496
On tree page 23 cell 6: invalid page number 3865
On tree page 23 cell 5: invalid page number 3232
On tree page 23 cell 4: invalid page number 2600
On tree page 23 cell 3: invalid page number 1969
Error: stepping, database disk image is malformed (11)

That probably means that something went wrong when the file was copied from somewhere.
-- Nick

I see, thank you for checking!