Hi Zeyu, Thanks for your question and for your interest in the TPP.
Yes I use MSFragger in the TPP and I did run into this exact problem last week. It required me to install java 9 jdk that I downloaded and installed from oracle. I then had to make sure that the windows PATH pointed to the correct version of java from the jdk. Let me know if you cannot find it and I would be glad to help you further. I have found that the PeptideProphet model that seems to function best for MSFragger searches is the EXPECTSCORE based NONPARAM (semi-supervised) model, also with the option ONEFVAL to model all the charge states with a single f-value mixture model. Hope you find this useful. Cheers! -David On Fri, May 10, 2024 at 3:05 PM Zeyu Wang <wangzeyuu...@gmail.com> wrote: > Hi, > > Do you use MSFragger in TPP? I downloaded MSFragger 4.0 and renamed it, > then placed it in this path: C:/TPP/bin/msfragger/msfragger.jar. However, > when I search my files, it seems to report an error related to the JRE > version. But MSFragger desktop GUI runs fine: > > Error: A JNI error has occurred, please check your installation and try > again. > Exception in thread "main" java.lang.UnsupportedClassVersionError: > edu/umich/andykong/msfragger/MSFragger has been compiled by a more recent > version of the Java Runtime (class file version 53.0), this version of the > Java Runtime only recognizes class file versions up to 52.0. > at java.lang.ClassLoader.defineClass1(Native Method) > at java.lang.ClassLoader.defineClass(Unknown Source) > at java.security.SecureClassLoader.defineClass(Unknown Source) > at java.net.URLClassLoader.defineClass(Unknown Source) > at java.net.URLClassLoader.access$100(Unknown Source) > at java.net.URLClassLoader$1.run(Unknown Source) > at java.net.URLClassLoader$1.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(Unknown Source) > at java.lang.ClassLoader.loadClass(Unknown Source) > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) > at java.lang.ClassLoader.loadClass(Unknown Source) > at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source) > > > Thank you! > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/ec3ab6d9-4563-44d8-9e12-65b1f16348d5n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/ec3ab6d9-4563-44d8-9e12-65b1f16348d5n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D_JpQxqRjeoAYmTVRThyt0Z%3DNDpCjNS-F5hWSs5akaMAQ%40mail.gmail.com.
