Question:

[JAEYOONSUNG]

Is there truly no significant spectra in my data?
Or could there be an issue with the settings during the analysis or with the FASTA file?
I would appreciate it if you could check
log.zip

[hbarsnes]

The problem seems to be your mzML files. Please make sure that they contain valid spectra that can be identified by the search engines. Maybe you can try converting the mzML files to mgf first and then inspect the mgf files manually to see if they contain any spectra that seems like they could be identified? You can for example use ThermoRawFileParserGUI for the conversion.