What type of mass spectrometer did the data files that you are trying to search come from?

The error that I am seeing in the EncyclopeDIA output is "Null pointer found when creating stripe object" and I also see "isolationWindowTarget=null", which makes me think that the problem is that there is an MS2 spectrum which has no precursor m/z.

If you would like, you could send us your files and we can try to figure out what is going wrong. You should send us your Skyline document, your raw files and your FASTA file.

In Skyline you can use the menu item:
File > Share
to create a .sky.zip file containing your Skyline document.
You can put that .sky.zip into a bigger .zip file along with your raw files and your FASTA file.

You can upload that big zip file here:
https://skyline.ms/files.url
-- Nick