Skyline DIA spec. library - FragPipe DDA data analysis issues

Skyline DIA spec. library - FragPipe DDA data analysis issues amey shirolkar  2022-05-12

hello Team,

After running for a sufficient time our latest runs in FragPipe (DIA Skyline spec library v/s DDA raw data files) it abruptly ends mentioning MSFragger or JAVA errors how to tackle this?
Screenshots are attached.
Please help.


Amey, PhD

Nick Shulman responded:  2022-05-13
I am not sure whether anyone on this support board is an expert on debugging FragPipe problems.
What program is shown in that screenshot?

The error that you are getting from MSFragger is not very helpful because the compiled code has been run through a "minimizer" which means that the names of things have been changed to be as small as possible. So, you're getting an error in a method which is now called "A.a". If we knew what the name of that method before it had been minimized, that would probably give us a good hint as to what is going on.

Where did you install your software from? It might be possible to find or build you a version of that software which gives better information when the error happens.
-- Nick